Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002104.1 Hibiscus syriacus cultivar Beakdansim tig00004304_pilon, 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: 55098
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:6197 original size:19 final size:20
Alignment explanation
Indices: 6170--6207 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
6160 ATAGCACATA
*
6170 AATCTATGCAAGT-ATACAC
1 AATCGATGCAAGTAATACAC
6189 AATCGATGCAAGTAATACA
1 AATCGATGCAAGTAATACA
6208 GTAGTGAGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.45, C:0.18, G:0.13, T:0.24
Consensus pattern (20 bp):
AATCGATGCAAGTAATACAC
Found at i:10207 original size:15 final size:15
Alignment explanation
Indices: 10187--10215 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
10177 TGATTCCAGA
10187 ATCTAAACACAAAAC
1 ATCTAAACACAAAAC
10202 ATCTAAACACAAAA
1 ATCTAAACACAAAA
10216 TATAATCCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.62, C:0.24, G:0.00, T:0.14
Consensus pattern (15 bp):
ATCTAAACACAAAAC
Found at i:13602 original size:30 final size:30
Alignment explanation
Indices: 13568--13649 Score: 101
Period size: 30 Copynumber: 2.7 Consensus size: 30
13558 GGAAGAACCT
*
13568 AAATAGCAAAAATAGAAATTTAATGGACTA
1 AAATAGCAAAAATAGAAATTTAAAGGACTA
* * *
13598 AAATAGCAAATATAGAAACTTAAAGGATTA
1 AAATAGCAAAAATAGAAATTTAAAGGACTA
* * *
13628 AAATAGCTAAAACATAAATTTA
1 AAATAGCAAAAATAGAAATTTA
13650 GAGGGTTGAA
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.57, C:0.07, G:0.11, T:0.24
Consensus pattern (30 bp):
AAATAGCAAAAATAGAAATTTAAAGGACTA
Found at i:15184 original size:31 final size:31
Alignment explanation
Indices: 15148--15206 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
15138 AACTTAAAAG
* *
15148 AGTTTTGCAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
15179 AGTTTTACAATACTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
15207 CCATACAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.42
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:15282 original size:22 final size:22
Alignment explanation
Indices: 15233--15281 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
15223 ATAAATTATT
**
15233 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
15255 TAAAATAAATCAATCTATACTAA
1 TAAAATAAATCAATCCATA-TAA
15278 TAAA
1 TAAA
15282 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:15372 original size:14 final size:14
Alignment explanation
Indices: 15355--15408 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
15345 CAATCTATAC
15355 AAATAAATTATTTA
1 AAATAAATTATTTA
* *
15369 AAATAAATCAGTCCATA
1 AAATAAATTA-T--TTA
15386 CAAATAAATTATTTA
1 -AAATAAATTATTTA
15401 AAATAAAT
1 AAATAAAT
15409 CAATCCATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
14 17 0.53
15 3 0.09
17 3 0.09
18 9 0.28
ACGTcount: A:0.57, C:0.07, G:0.02, T:0.33
Consensus pattern (14 bp):
AAATAAATTATTTA
Found at i:15372 original size:32 final size:32
Alignment explanation
Indices: 15333--15525 Score: 201
Period size: 32 Copynumber: 6.7 Consensus size: 32
15323 CAATCTATAT
*
15333 TTTAAAATAAATCAATCTATACAAATAAATTA
1 TTTAAAATAAATCAATCCATACAAATAAATTA
*
15365 TTTAAAATAAATCAGTCCATACAAATAAATTA
1 TTTAAAATAAATCAATCCATACAAATAAATTA
15397 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACAAATAAATTA
*
15419 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACAAATAAATTA
15451 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACAAATAAATTA
*
15473 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACAAATAAATTA
*
15505 TTTAAAATAAACCAATCCATA
1 TTTAAAATAAATCAATCCATA
15526 TTTAAAATAA
Statistics
Matches: 137, Mismatches: 4, Indels: 40
0.76 0.02 0.22
Matches are distributed among these distances:
22 32 0.23
23 4 0.03
24 2 0.01
26 6 0.04
28 6 0.04
30 2 0.01
31 4 0.03
32 81 0.59
ACGTcount: A:0.53, C:0.13, G:0.01, T:0.34
Consensus pattern (32 bp):
TTTAAAATAAATCAATCCATACAAATAAATTA
Found at i:15423 original size:22 final size:22
Alignment explanation
Indices: 15397--15439 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
15387 AAATAAATTA
15397 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
15419 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
15440 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:15448 original size:22 final size:22
Alignment explanation
Indices: 15399--15447 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
15389 ATAAATTATT
**
15399 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
15421 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
15444 TAAA
1 TAAA
15448 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:15477 original size:22 final size:22
Alignment explanation
Indices: 15451--15493 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
15441 TAATAAATTA
15451 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
15473 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
15494 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:15502 original size:22 final size:22
Alignment explanation
Indices: 15453--15501 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
15443 ATAAATTATT
**
15453 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
15475 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
15498 TAAA
1 TAAA
15502 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:15509 original size:86 final size:83
Alignment explanation
Indices: 15235--15525 Score: 319
Period size: 86 Copynumber: 3.5 Consensus size: 83
15225 AAATTATTTA
* *
15235 AAATAAATCAATC-CATAT-TTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATC
1 AAATAAATCAATCTAATATATTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATC
* *
15298 AATCCATACAACTACAAT
66 AATCCATACAAATAAAAT
* *
15316 -AATAAATCAATCT-ATAT-TTTAAAATAAATCAATCTATACAAATAAATTATTTAAAATAAATC
1 AAATAAATCAATCTAATATATTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATC
*
15378 AGTCCATACAAATAAATTATTT
66 AATCCATACAAATAAA--A--T
*
15400 AAAATAAATCAATC-CATAT-TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAAT
1 -AAATAAATCAATCTAATATATTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAAT
***
15463 CAATCCATA-TTTTAAAAT
65 CAATCCATACAAATAAAAT
* * *
15481 AAATCAATCCATACTAATAAATTATTTAAAATAAACCAATCCATA
1 AAATAAATCAAT-CTAAT--A-TATTTAAAATAAATCAATCCATA
15526 TTTAAAATAA
Statistics
Matches: 182, Mismatches: 14, Indels: 23
0.83 0.06 0.11
Matches are distributed among these distances:
80 83 0.46
81 2 0.01
82 3 0.02
83 1 0.01
84 2 0.01
85 5 0.03
86 86 0.47
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.33
Consensus pattern (83 bp):
AAATAAATCAATCTAATATATTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATC
AATCCATACAAATAAAAT
Found at i:15529 original size:21 final size:21
Alignment explanation
Indices: 15503--15546 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
15493 ACTAATAAAT
15503 TATTTAAAATAAACCAATCCA
1 TATTTAAAATAAACCAATCCA
*
15524 TATTTAAAATAAATCAATCCA
1 TATTTAAAATAAACCAATCCA
15545 TA
1 TA
15547 CTAATAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (21 bp):
TATTTAAAATAAACCAATCCA
Found at i:15578 original size:15 final size:15
Alignment explanation
Indices: 15549--15696 Score: 172
Period size: 15 Copynumber: 9.5 Consensus size: 15
15539 AATCCATACT
15549 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
15563 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
15578 AATAAATCAATTCATATTTTAT
1 AAT--A--AA-T--TATTTTAA
* *
15600 AACAATTTATTTTAA
1 AATAAATTATTTTAA
*
15615 AATAAATTATTTTAT
1 AATAAATTATTTTAA
*
15630 AATAAATTATTTTAT
1 AATAAATTATTTTAA
15645 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
15660 AATAAATTATTTTAT
1 AATAAATTATTTTAA
15675 AATAAATTATTTTAA
1 AATAAATTATTTTAA
15690 AATAAAT
1 AATAAAT
15697 AACCTTATTA
Statistics
Matches: 116, Mismatches: 10, Indels: 15
0.82 0.07 0.11
Matches are distributed among these distances:
14 9 0.08
15 91 0.78
17 2 0.02
18 1 0.01
19 2 0.02
20 2 0.02
22 9 0.08
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:15608 original size:47 final size:48
Alignment explanation
Indices: 15355--15681 Score: 238
Period size: 54 Copynumber: 6.5 Consensus size: 48
15345 CAATCTATAC
* * *
15355 AAATAAATTA-TTTAAAATAAATCAGTCCATACAAATAAATTA-TTTA
1 AAATAAATTATTTTAAAATAAATCAATCCATACTAATAAAATATTTTA
*
15401 AAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTA-TTTA
1 AAAT--A--AAT---TATTTTAAAATAAATCAATCCATACTAATAAAATATTTTA
*
15455 AAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTA-TTTA
1 AAAT--A--AAT---TATTTTAAAATAAATCAATCCATACTAATAAAATATTTTA
* *
15509 AAATAAACCAATCCATATTTAAAATAAATCAATCCATACTAATAAATTA-TTTA
1 AAAT--A--AAT-TAT-TTTAAAATAAATCAATCCATACTAATAAAATATTTTA
* * *
15562 AAATAAATTATTTTAAAATAAATCAATTCATATTTTATAACAATTTATTTTA
1 AAATAAATTATTTTAAAATAAATCAATCCATA-CTAATAA-AA--TATTTTA
* * ** *
15614 AAATAAATTATTTTATAATAAAT-TAT-TTTA-TAATAAATTATTTTA
1 AAATAAATTATTTTAAAATAAATCAATCCATACTAATAAAATATTTTA
*
15659 AAATAAATTATTTTATAATAAAT
1 AAATAAATTATTTTAAAATAAAT
15682 TATTTTAAAA
Statistics
Matches: 251, Mismatches: 16, Indels: 29
0.85 0.05 0.10
Matches are distributed among these distances:
45 30 0.12
46 4 0.02
47 21 0.08
48 13 0.05
49 4 0.02
50 5 0.02
51 5 0.02
52 28 0.11
53 42 0.17
54 99 0.39
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (48 bp):
AAATAAATTATTTTAAAATAAATCAATCCATACTAATAAAATATTTTA
Found at i:16201 original size:42 final size:41
Alignment explanation
Indices: 16087--16203 Score: 180
Period size: 42 Copynumber: 2.8 Consensus size: 41
16077 CCCCGAATTC
* *
16087 CCGTGTTTGTTTCACGTAATTCGTTTTTCGAAAAATGTTTT
1 CCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTTT
16128 CCTGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTTT
1 CC-GTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTTT
* *
16170 CTCGTGTTTGCTTCACGTAATTGGTTTTCCGGAA
1 C-CGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
16204 TGTAATTCAT
Statistics
Matches: 70, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
41 2 0.03
42 67 0.96
43 1 0.01
ACGTcount: A:0.17, C:0.17, G:0.20, T:0.46
Consensus pattern (41 bp):
CCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTTT
Found at i:16415 original size:22 final size:22
Alignment explanation
Indices: 16390--16438 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 22
16380 ATTATTTATT
16390 TATT-TATTAATATTTATAATAA
1 TATTATATT-ATATTTATAATAA
16412 TATTATATTATATTT-T--TAA
1 TATTATATTATATTTATAATAA
16431 TATTATAT
1 TATTATAT
16439 AAAATAATCA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
19 11 0.42
21 1 0.04
22 10 0.38
23 4 0.15
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
TATTATATTATATTTATAATAA
Found at i:16583 original size:23 final size:23
Alignment explanation
Indices: 16557--16601 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
16547 AATAATATTT
16557 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
16580 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
16602 ATATAACACT
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:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:17064 original size:3 final size:3
Alignment explanation
Indices: 17058--17097 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
17048 AACATACCCT
17058 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -AA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
17098 TTTTTGTAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:19041 original size:15 final size:15
Alignment explanation
Indices: 19013--19054 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 15
19003 AGACTTGTTA
19013 TTTATATTGGTATTT
1 TTTATATTGGTATTT
*
19028 TTTA-ATTGG--TTA
1 TTTATATTGGTATTT
19040 TTTATATTGGTATTT
1 TTTATATTGGTATTT
19055 AACTATCATG
Statistics
Matches: 22, Mismatches: 2, Indels: 6
0.73 0.07 0.20
Matches are distributed among these distances:
12 6 0.27
13 5 0.23
14 5 0.23
15 6 0.27
ACGTcount: A:0.21, C:0.00, G:0.14, T:0.64
Consensus pattern (15 bp):
TTTATATTGGTATTT
Found at i:19050 original size:13 final size:12
Alignment explanation
Indices: 19011--19055 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 12
19001 GTAGACTTGT
19011 TATTTATATTGG
1 TATTTATATTGG
*
19023 TATTTTTTAATTGG
1 TA-TTTAT-ATTGG
19037 TTATTTATATTGG
1 -TATTTATATTGG
19050 TATTTA
1 TATTTA
19056 ACTATCATGT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
12 8 0.29
13 9 0.32
14 9 0.32
15 2 0.07
ACGTcount: A:0.24, C:0.00, G:0.13, T:0.62
Consensus pattern (12 bp):
TATTTATATTGG
Found at i:21325 original size:23 final size:24
Alignment explanation
Indices: 21263--21334 Score: 71
Period size: 23 Copynumber: 3.1 Consensus size: 24
21253 TTCTAATAAT
*
21263 TATATCTTCATGAC--GCATTTTTC
1 TATATCTTTATGACATG-ATTTTTC
*
21286 TATATTTTTATGACATGATTTTT-
1 TATATCTTTATGACATGATTTTTC
*
21309 TATATCTTTATGGCATG-TTTTCTC
1 TATATCTTTATGACATGATTTT-TC
21333 TA
1 TA
21335 CATTTTGACA
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
22 4 0.10
23 28 0.68
24 8 0.20
25 1 0.02
ACGTcount: A:0.22, C:0.14, G:0.10, T:0.54
Consensus pattern (24 bp):
TATATCTTTATGACATGATTTTTC
Found at i:25214 original size:19 final size:19
Alignment explanation
Indices: 25159--25217 Score: 57
Period size: 19 Copynumber: 3.2 Consensus size: 19
25149 AAATTTAACG
* *
25159 ACGGTCAACGGCCA-GTCA
1 ACGGTCAACGACTAGGTCA
* *
25177 AAGGTCAACGACTATGTCA
1 ACGGTCAACGACTAGGTCA
* *
25196 ACGGTCAACTACTGGGTCA
1 ACGGTCAACGACTAGGTCA
25215 ACG
1 ACG
25218 ACTCACCCAG
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
18 11 0.33
19 22 0.67
ACGTcount: A:0.31, C:0.27, G:0.25, T:0.17
Consensus pattern (19 bp):
ACGGTCAACGACTAGGTCA
Found at i:39560 original size:186 final size:184
Alignment explanation
Indices: 39122--39786 Score: 602
Period size: 186 Copynumber: 3.5 Consensus size: 184
39112 CCAAATTTAC
* ** * * * *
39122 TATACATATTCATAACAATTTTAGATTTTAACGTATTTTGTTATCGTGAG-ATTGTCAAAGGTCC
1 TATAGATATTCATAAC-ATTTTTTATTTTAACTTATTTTGTTATCGTGGGAAAT-TCAAAAG-CC
* * * * * *
39186 T-GTCAACTTAAAATCTAGTAATATTTTAGGCACAA-CTGATTTTATTAAACATAAAATTAACAT
63 TCGTCAACTTAAACTTTGGTAACATTTTAGGCGCAATC-GATATTATT-AACATAAAATTAACAT
* * * * * ** * * * ** *
39249 TTCAAATCGCAACCTACTAAGATTTCTTAGCGACCCCTAATATTCTTAGGCGCAATATGATTTAT
126 TCCAAATCACAA---AAT-A-CTTT-TTAACGACCTATAACATTCTTCGGCACAACCTGATTTCT
* * *
39314 TATAGATATTCGTAACATTTTTTATATTTTAACTTATTTTGTTATCGTGGGAAGTTCAAAAGCCA
1 TATAGATATTCATAACA-TTTTT-TATTTTAACTTATTTTGTTATCGTGGGAAATTCAAAAGCCT
* *
39379 CGCCAACTTAAACTTTGGTAACATTTTAAGCGCAATCGATATTATTAAACATAAAATTAACATTC
64 CGTCAACTTAAACTTTGGTAACATTTTAGGCGCAATCGATATTATT-AACATAAAATTAACATTC
* * * * *
39444 CAGATCACAAAATACCTTATTT-GCGA-CTCATAACATTTTTGGGCACAACTTGATTTCT
128 CAAATCACAAAATA-CTT-TTTAACGACCT-ATAACATTCTTCGGCACAACCTGATTTCT
* *
39502 TATAGATATTCATAACATTTTTTATTTTAACTTATTTTGTTGTAGTGGGAAATTCAAAAGCCTCG
1 TATAGATATTCATAACATTTTTTATTTTAACTTATTTTGTTATCGTGGGAAATTCAAAAGCCTCG
* * * * * * *
39567 TCAACTTAAAATTTGGTAACATTTTAGGTGCAATTGATTTTATTGACATAAAATTAGCATTTCAA
66 TCAACTTAAACTTTGGTAACATTTTAGGCGCAATCGATATTATTAACATAAAATTAACATTCCAA
** ** * ** *
39632 ATCGTAACTTACTTTTTAAATGACCTATAACATTCTTCGGTGCAACCTGGTTTCT
131 ATCACAAAATACTTTTT-AACGACCTATAACATTCTTCGGCACAACCTGATTTCT
* * *
39687 TATAGATATTCATTACATTTTTTATTTTAAACTTATTTTGTTATCGTGGGAAATTCAAAATCTTC
1 TATAGATATTCATAACATTTTTTATTTT-AACTTATTTTGTTATCGTGGGAAATTCAAAAGCCTC
* *
39752 ATCACCTTAAACTTTGGTAACATTTTAGGCGCAAT
65 GTCAACTTAAACTTTGGTAACATTTTAGGCGCAAT
39787 ATAATATGTT
Statistics
Matches: 394, Mismatches: 68, Indels: 28
0.80 0.14 0.06
Matches are distributed among these distances:
183 3 0.01
184 3 0.01
185 76 0.19
186 142 0.36
187 6 0.02
188 41 0.10
189 5 0.01
190 3 0.01
191 1 0.00
192 20 0.05
193 91 0.23
194 3 0.01
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (184 bp):
TATAGATATTCATAACATTTTTTATTTTAACTTATTTTGTTATCGTGGGAAATTCAAAAGCCTCG
TCAACTTAAACTTTGGTAACATTTTAGGCGCAATCGATATTATTAACATAAAATTAACATTCCAA
ATCACAAAATACTTTTTAACGACCTATAACATTCTTCGGCACAACCTGATTTCT
Found at i:47950 original size:35 final size:35
Alignment explanation
Indices: 47904--47978 Score: 150
Period size: 35 Copynumber: 2.1 Consensus size: 35
47894 TTCATGTTCA
47904 AAATTCCAAAATACTTTAATTATATTCTAAACCCT
1 AAATTCCAAAATACTTTAATTATATTCTAAACCCT
47939 AAATTCCAAAATACTTTAATTATATTCTAAACCCT
1 AAATTCCAAAATACTTTAATTATATTCTAAACCCT
47974 AAATT
1 AAATT
47979 AAAGTATTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.44, C:0.19, G:0.00, T:0.37
Consensus pattern (35 bp):
AAATTCCAAAATACTTTAATTATATTCTAAACCCT
Found at i:48022 original size:35 final size:35
Alignment explanation
Indices: 47974--48050 Score: 100
Period size: 35 Copynumber: 2.2 Consensus size: 35
47964 TCTAAACCCT
* *
47974 AAATTAAAGTATTTTAAAATTTAGGGTTTAAAATG
1 AAATTGAATTATTTTAAAATTTAGGGTTTAAAATG
* ** *
48009 TAATTGAATTATTTTGGAATTTAGGGTTTAGAATG
1 AAATTGAATTATTTTAAAATTTAGGGTTTAAAATG
48044 AAATTGA
1 AAATTGA
48051 GGAATGTGTT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.40, C:0.00, G:0.18, T:0.42
Consensus pattern (35 bp):
AAATTGAATTATTTTAAAATTTAGGGTTTAAAATG
Found at i:54729 original size:21 final size:21
Alignment explanation
Indices: 54703--54755 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
54693 AGAATAATGT
*
54703 AAATATATCAATTTA-AATATA
1 AAATATATCAATATATAATA-A
* *
54724 AAATATTTTAATATATAATAA
1 AAATATATCAATATATAATAA
54745 AAATATATCAA
1 AAATATATCAA
54756 ATTACATAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 22 0.85
22 4 0.15
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (21 bp):
AAATATATCAATATATAATAA
Done.