Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001499.1 Hibiscus syriacus cultivar Beakdansim tig00002938_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: 124001
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1879 original size:29 final size:30
Alignment explanation
Indices: 1809--1883 Score: 89
Period size: 31 Copynumber: 2.5 Consensus size: 30
1799 ATTATAATAT
** *
1809 AAAATACTTTATGTATCTATTTTGTCTAAA
1 AAAATACTTTAAATATCTATTTTGTATAAA
* *
1839 AAGATAACTTTAAATATTTATTTTG-ATAAA
1 AAAAT-ACTTTAAATATCTATTTTGTATAAA
1869 AAAATACTTTAAATA
1 AAAATACTTTAAATA
1884 CTTAAATAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 10 0.26
30 12 0.32
31 16 0.42
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.43
Consensus pattern (30 bp):
AAAATACTTTAAATATCTATTTTGTATAAA
Found at i:3809 original size:11 final size:10
Alignment explanation
Indices: 3776--3809 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
3766 ATCGAAATGC
3776 AAATG-AAAT
1 AAATGAAAAT
3785 AAATGAAAAT
1 AAATGAAAAT
3795 AAATGAAATAT
1 AAATGAAA-AT
3806 AAAT
1 AAAT
3810 ATAAAATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 5 0.22
10 12 0.52
11 6 0.26
ACGTcount: A:0.68, C:0.00, G:0.09, T:0.24
Consensus pattern (10 bp):
AAATGAAAAT
Found at i:3850 original size:12 final size:13
Alignment explanation
Indices: 3800--3854 Score: 53
Period size: 13 Copynumber: 4.3 Consensus size: 13
3790 AAAATAAATG
*
3800 AAATATAAAT-AT
1 AAATATATATAAT
3812 AAAATATATATATAT
1 -AAATATATATA-AT
*
3827 ATATATATATAAT
1 AAATATATATAAT
3840 AAAT-TATATAA-
1 AAATATATATAAT
3851 AAAT
1 AAAT
3855 TAATAGTATT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
11 4 0.11
12 7 0.19
13 14 0.38
14 10 0.27
15 2 0.05
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
AAATATATATAAT
Found at i:3925 original size:19 final size:20
Alignment explanation
Indices: 3888--3926 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
3878 AATATTAATA
3888 TATTCTAAATAAAATTATAT
1 TATTCTAAATAAAATTATAT
3908 TATTCTAAATAAAA-TATAT
1 TATTCTAAATAAAATTATAT
3927 AAATAAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (20 bp):
TATTCTAAATAAAATTATAT
Found at i:6280 original size:14 final size:14
Alignment explanation
Indices: 6256--6286 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
6246 ATAATAAATA
*
6256 ATTATGAATATATT
1 ATTATAAATATATT
6270 ATTATAAATATATT
1 ATTATAAATATATT
6284 ATT
1 ATT
6287 TTAATTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (14 bp):
ATTATAAATATATT
Found at i:9361 original size:21 final size:21
Alignment explanation
Indices: 9319--9361 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
9309 AATATATTTT
*
9319 AAATTATTAAAAAACTGTAAA
1 AAATTATTAAAAAACAGTAAA
9340 AAATTATTAAAAAATCAG-AAA
1 AAATTATTAAAAAA-CAGTAAA
9361 A
1 A
9362 TACAAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 18 0.90
22 2 0.10
ACGTcount: A:0.65, C:0.05, G:0.05, T:0.26
Consensus pattern (21 bp):
AAATTATTAAAAAACAGTAAA
Found at i:26368 original size:55 final size:56
Alignment explanation
Indices: 26308--26432 Score: 171
Period size: 55 Copynumber: 2.2 Consensus size: 56
26298 ACACCCCTCT
*
26308 GGTGGATCCTATGCTTCGGCTAGGATAAGTCCTTATGGACCCACG-TGCTCCCTTA
1 GGTGGATCCTATGCTTCGGCTAGGATAAGTCCTTATAGACCCACGATGCTCCCTTA
** * * *
26363 GGTGGATCCTACACTTCTGCTAGGTTAAGTCTTTATAGACCCACGATGCTCCCTTA
1 GGTGGATCCTATGCTTCGGCTAGGATAAGTCCTTATAGACCCACGATGCTCCCTTA
*
26419 GGTTGGCTCCTATG
1 GG-TGGATCCTATG
26433 TTCAATGAGC
Statistics
Matches: 59, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
55 39 0.66
56 12 0.20
57 8 0.14
ACGTcount: A:0.18, C:0.26, G:0.24, T:0.31
Consensus pattern (56 bp):
GGTGGATCCTATGCTTCGGCTAGGATAAGTCCTTATAGACCCACGATGCTCCCTTA
Found at i:28986 original size:20 final size:20
Alignment explanation
Indices: 28950--28992 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
28940 GGACTTATTT
28950 AATTTTTTAAAAAAATA-AA
1 AATTTTTTAAAAAAATATAA
**
28969 AATTTATTTAAATTAATATAA
1 AATTT-TTTAAAAAAATATAA
28990 AAT
1 AAT
28993 ATAAAATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 5 0.25
20 10 0.50
21 5 0.25
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
AATTTTTTAAAAAAATATAA
Found at i:29274 original size:15 final size:15
Alignment explanation
Indices: 29254--29303 Score: 50
Period size: 14 Copynumber: 3.4 Consensus size: 15
29244 ATACTAGAAA
29254 TATTTTTTTATATTT
1 TATTTTTTTATATTT
*
29269 TA-TTTTTCATATTT
1 TATTTTTTTATATTT
* *
29283 TACTTGTTTT-TGTTT
1 TA-TTTTTTTATATTT
29298 TATTTT
1 TATTTT
29304 CTTAGAAATT
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
14 16 0.57
15 8 0.29
16 4 0.14
ACGTcount: A:0.16, C:0.04, G:0.04, T:0.76
Consensus pattern (15 bp):
TATTTTTTTATATTT
Found at i:30224 original size:14 final size:14
Alignment explanation
Indices: 30205--30231 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
30195 CTTCTTGAAA
30205 GTCCAATCAACAAC
1 GTCCAATCAACAAC
30219 GTCCAATCAACAA
1 GTCCAATCAACAA
30232 TTCTAGAAGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.33, G:0.07, T:0.15
Consensus pattern (14 bp):
GTCCAATCAACAAC
Found at i:38006 original size:31 final size:31
Alignment explanation
Indices: 37970--38028 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
37960 AACTTAAAAG
* *
37970 AGTTTTGCAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
38001 AGTTTTACAATACTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
38029 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:38132 original size:22 final size:22
Alignment explanation
Indices: 38106--38148 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
38096 CTAAAAATTA
38106 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
38128 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
38149 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:38157 original size:22 final size:22
Alignment explanation
Indices: 38108--38156 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
38098 AAAAATTATT
**
38108 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
38130 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
38153 TAAA
1 TAAA
38157 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:38164 original size:32 final size:32
Alignment explanation
Indices: 38128--38455 Score: 307
Period size: 32 Copynumber: 11.7 Consensus size: 32
38118 CAATCCATAT
38128 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
38160 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
38192 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
38214 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
38246 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
38268 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
38300 TTTAAAATAAATCAATCCATAC-AACTACA--A
1 TTTAAAATAAATCAATCCATACTAA-TAAATTA
38330 --T--AATAAATCAATCCATA-T--T---TTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
38352 --T-AATTAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
38381 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
38403 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
38435 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
38456 TTTTAAAATA
Statistics
Matches: 249, Mismatches: 3, Indels: 88
0.73 0.01 0.26
Matches are distributed among these distances:
22 50 0.20
23 22 0.09
24 4 0.02
26 26 0.10
28 10 0.04
29 3 0.01
30 4 0.02
31 9 0.04
32 121 0.49
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (32 bp):
TTTAAAATAAATCAATCCATACTAATAAATTA
Found at i:38180 original size:54 final size:54
Alignment explanation
Indices: 38043--38476 Score: 401
Period size: 54 Copynumber: 8.0 Consensus size: 54
38033 ACAACTACAA
*
38043 TAATAAATTATTTAAAATAAATCAATCCACATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
38097 TAA-AAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
** * ** * **
38150 TAATAAATTATTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAAT-C
1 TAATAAATTATTTAAAATAAATCAATCCATA-TTTTAAAATAAAT-CAATCCATAC
** ** * ** * **
38205 -AATCCA-TATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAAT-C
1 TAATAAATTA-TTTAAAATAAATCAATCCATA-TTTTAAAATAAAT-CAATCCATAC
**
38259 -AATCCA-TATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAC
1 TAATAAATTA-TTTAAAATAAATCAAT-C---C--AT--A-T-TTTAAAATAAATCAATCCATAC
* *
38322 -AACTACA--A--T--AATAAATCAATCCATATTTTATAATTAAATCAATCCATAC
1 TAA-TAAATTATTTAAAATAAATCAATCCATATTTTA-AAATAAATCAATCCATAC
38371 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
38425 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCAT
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCAT
38477 TATTTTAAAA
Statistics
Matches: 333, Mismatches: 24, Indels: 46
0.83 0.06 0.11
Matches are distributed among these distances:
48 4 0.01
49 21 0.06
50 3 0.01
51 1 0.00
52 2 0.01
53 55 0.17
54 174 0.52
55 31 0.09
56 5 0.02
57 1 0.00
58 12 0.04
60 3 0.01
62 7 0.02
63 11 0.03
64 3 0.01
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.35
Consensus pattern (54 bp):
TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
Found at i:38218 original size:22 final size:22
Alignment explanation
Indices: 38192--38234 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
38182 TAATAAATTA
38192 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
38214 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
38235 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:38243 original size:22 final size:22
Alignment explanation
Indices: 38194--38242 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
38184 ATAAATTATT
**
38194 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
38216 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
38239 TAAA
1 TAAA
38243 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:38272 original size:22 final size:22
Alignment explanation
Indices: 38246--38288 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
38236 TAATAAATTA
38246 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
38268 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
38289 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:38297 original size:22 final size:22
Alignment explanation
Indices: 38248--38296 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
38238 ATAAATTATT
**
38248 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
38270 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
38293 TAAA
1 TAAA
38297 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:38379 original size:23 final size:24
Alignment explanation
Indices: 38307--38380 Score: 73
Period size: 23 Copynumber: 3.1 Consensus size: 24
38297 TTATTTAAAA
38307 TAAATCAATCCATAC-AACTACAAT
1 TAAATCAATCCATACTAA-TACAAT
** *
38331 AATAAATCAATCCATA-TTTTATAAT
1 --TAAATCAATCCATACTAATACAAT
38356 TAAATCAATCCATACTAATA-AAT
1 TAAATCAATCCATACTAATACAAT
38379 TA
1 TA
38381 TTTAAAATAA
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
23 19 0.46
24 3 0.07
25 5 0.12
26 14 0.34
ACGTcount: A:0.50, C:0.18, G:0.00, T:0.32
Consensus pattern (24 bp):
TAAATCAATCCATACTAATACAAT
Found at i:38382 original size:81 final size:80
Alignment explanation
Indices: 38251--38401 Score: 284
Period size: 81 Copynumber: 1.9 Consensus size: 80
38241 AATTATTTAA
38251 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
38316 CCATACAACTACAAT
66 CCATACAACTACAAT
*
38331 AATAAATCAATCCATATTTTATAATTAAATCAATCCATACTAATAAATTATTTAAAATAAATCAA
1 AATAAATCAATCCATATTTTA-AAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAA
38396 TCCATA
65 TCCATA
38402 TTTTAAAATA
Statistics
Matches: 69, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
80 21 0.30
81 48 0.70
ACGTcount: A:0.52, C:0.15, G:0.00, T:0.33
Consensus pattern (80 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
CCATACAACTACAAT
Found at i:38407 original size:22 final size:22
Alignment explanation
Indices: 38381--38423 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
38371 TAATAAATTA
38381 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
38403 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
38424 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:38432 original size:22 final size:22
Alignment explanation
Indices: 38383--38431 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
38373 ATAAATTATT
**
38383 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
38405 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
38428 TAAA
1 TAAA
38432 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:38484 original size:23 final size:22
Alignment explanation
Indices: 38435--38511 Score: 136
Period size: 22 Copynumber: 3.5 Consensus size: 22
38425 TAATAAATTA
38435 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
38457 TTTAAAATAAATCAATCCATTAT
1 TTTAAAATAAATCAATCCA-TAT
38480 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
38502 TTTATAATAA
1 TTTAAAATAA
38512 TTTATTTTAA
Statistics
Matches: 53, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
22 31 0.58
23 22 0.42
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.39
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:38511 original size:135 final size:131
Alignment explanation
Indices: 38053--38500 Score: 711
Period size: 135 Copynumber: 3.3 Consensus size: 131
38043 TAATAAATTA
*
38053 TTTAAAATAAATCAATCCACATTTTAAAATAAATCAATCCATACTAA-AAATTATTTAAAATAAA
1 TTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAA
38117 TCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAC
66 TCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT-C---C
38182 TAATAAATT
127 --AT-AA-T
38191 ATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAA
1 -TTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAA
38256 ATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATA
65 ATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCAT-
*
38321 CAAC
129 -AAT
** *
38325 TACAATAATAAATCAATCCATATTTTATAATTAAATCAATCCATACTAATAAATTATTTAAAATA
1 TTTAA-AATAAATCAATCCATATTTTA-AAATAAATCAATCCATACTAATAAATTATTTAAAATA
38390 AATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCAT
64 AATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCAT
38455 -AT
129 AAT
38457 TTTAAAATAAATCAATCCATTATTTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCA-TATTTTAAAATAAATCAATCCATA
38501 TTTTATAATA
Statistics
Matches: 294, Mismatches: 10, Indels: 18
0.91 0.03 0.06
Matches are distributed among these distances:
131 30 0.10
132 11 0.04
133 3 0.01
134 23 0.08
135 103 0.35
136 1 0.00
139 47 0.16
140 76 0.26
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.35
Consensus pattern (131 bp):
TTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAA
TCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAA
T
Found at i:38519 original size:15 final size:15
Alignment explanation
Indices: 38499--38618 Score: 213
Period size: 15 Copynumber: 8.0 Consensus size: 15
38489 AATCAATCCA
* *
38499 TATTTTATAATAATT
1 TATTTTAAAATAAAT
38514 TATTTTAAAATAAAT
1 TATTTTAAAATAAAT
38529 TATTTTAAAATAAAT
1 TATTTTAAAATAAAT
*
38544 TATTTTATAATAAAT
1 TATTTTAAAATAAAT
38559 TATTTTAAAATAAAT
1 TATTTTAAAATAAAT
38574 TATTTTAAAATAAAT
1 TATTTTAAAATAAAT
38589 TATTTTAAAATAAAT
1 TATTTTAAAATAAAT
38604 TATTTTAAAATAAAT
1 TATTTTAAAATAAAT
38619 AACCTTATTA
Statistics
Matches: 101, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 101 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
TATTTTAAAATAAAT
Found at i:38935 original size:23 final size:23
Alignment explanation
Indices: 38892--38935 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
38882 TGTATATATT
* *
38892 TTTCGTCACATATTGTTAAACAA
1 TTTCGTCACATAATGTCAAACAA
38915 TTTCGTCAC-TAAATGTCAAAC
1 TTTCGTCACAT-AATGTCAAAC
38936 CTTTGTTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 1 0.06
23 17 0.94
ACGTcount: A:0.34, C:0.20, G:0.09, T:0.36
Consensus pattern (23 bp):
TTTCGTCACATAATGTCAAACAA
Found at i:39102 original size:18 final size:19
Alignment explanation
Indices: 39065--39102 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
39055 TCTTAAACGT
* *
39065 TCTATTATTTTATTATAAA
1 TCTAATATTTTATAATAAA
39084 TCTAATATTTT-TAATAAA
1 TCTAATATTTTATAATAAA
39102 T
1 T
39103 TATCAATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.55
Consensus pattern (19 bp):
TCTAATATTTTATAATAAA
Found at i:42592 original size:20 final size:20
Alignment explanation
Indices: 42567--42613 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
42557 TATTCTCTCG
42567 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCAAATTCGCA
** *
42587 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCAAATTCGCA
42607 TTGCGAT
1 TTGCGAT
42614 TTTGTTGTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.36
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCA
Found at i:42634 original size:34 final size:34
Alignment explanation
Indices: 42587--42680 Score: 118
Period size: 33 Copynumber: 2.8 Consensus size: 34
42577 CAAATTCGCA
* * * *
42587 TTGCGATAGTCATTTTCGCGTTGCGATTTTGTTG
1 TTGCGATAGTCATTTTCGCATTGCGATTCTCTCG
**
42621 TTGCGATTTTCA-TTTCGCATTGCGATTCTCTCG
1 TTGCGATAGTCATTTTCGCATTGCGATTCTCTCG
*
42654 TTGCAATAGTCATTTTCGCATTGCGAT
1 TTGCGATAGTCATTTTCGCATTGCGAT
42681 AGTCATTTTC
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
33 26 0.52
34 24 0.48
ACGTcount: A:0.15, C:0.19, G:0.21, T:0.45
Consensus pattern (34 bp):
TTGCGATAGTCATTTTCGCATTGCGATTCTCTCG
Found at i:42682 original size:20 final size:20
Alignment explanation
Indices: 42654--42700 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
42644 GATTCTCTCG
*
42654 TTGCAATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
42674 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
42694 TTGCGAT
1 TTGCGAT
42701 TTTAAGTTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.40
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:44665 original size:14 final size:14
Alignment explanation
Indices: 44646--44681 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
44636 ATTGTTTAAT
44646 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
44660 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
44674 TGATTTGT
1 TGATTTGT
44682 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:44880 original size:20 final size:20
Alignment explanation
Indices: 44855--45050 Score: 77
Period size: 20 Copynumber: 9.8 Consensus size: 20
44845 GTGAAATTAG
44855 TTTCGCGTTGCGATTTTCAT
1 TTTCGCGTTGCGATTTTCAT
*
44875 TTTCGCATTGCGA--TTCA-
1 TTTCGCGTTGCGATTTTCAT
*
44892 ---CTCGTTGCGATTTTCA-
1 TTTCGCGTTGCGATTTTCAT
* *
44908 TTTCGCATTGCGATTCTCA-
1 TTTCGCGTTGCGATTTTCAT
*
44927 TTTCGCATTGCGATTCTCTCGTTGCGAT
1 TTTCGCGTTGCGA---T-T--TT-C-AT
* * **
44955 TCTCTCGTTGCGATGGTCAT
1 TTTCGCGTTGCGATTTTCAT
* **
44975 TTCCGCGTTGCGATAGTCA-
1 TTTCGCGTTGCGATTTTCAT
* **
44994 ATTCTGCGTTGCGATAGTCAT
1 TTTC-GCGTTGCGATTTTCAT
* **
45015 TTTCGTGTTGCGATAGTCAT
1 TTTCGCGTTGCGATTTTCAT
*
45035 ATTCGCGTTGCGATTT
1 TTTCGCGTTGCGATTT
45051 CCGCGTTGCG
Statistics
Matches: 136, Mismatches: 24, Indels: 32
0.71 0.12 0.17
Matches are distributed among these distances:
14 8 0.06
16 4 0.03
18 4 0.03
19 28 0.21
20 71 0.52
21 4 0.03
22 2 0.01
23 1 0.01
25 2 0.01
26 1 0.01
27 1 0.01
28 10 0.07
ACGTcount: A:0.14, C:0.22, G:0.22, T:0.42
Consensus pattern (20 bp):
TTTCGCGTTGCGATTTTCAT
Found at i:44917 original size:33 final size:34
Alignment explanation
Indices: 44860--44923 Score: 121
Period size: 33 Copynumber: 1.9 Consensus size: 34
44850 ATTAGTTTCG
44860 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
44894 CGTTGCGATTTTCA-TTTCGCATTGCGATTC
1 CGTTGCGATTTTCATTTTCGCATTGCGATTC
44924 TCATTTCGCA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 16 0.53
34 14 0.47
ACGTcount: A:0.14, C:0.23, G:0.19, T:0.44
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
Found at i:44920 original size:19 final size:19
Alignment explanation
Indices: 44855--44941 Score: 103
Period size: 19 Copynumber: 4.8 Consensus size: 19
44845 GTGAAATTAG
*
44855 TTTCGCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
44874 TTTTCGCATTGCGA--TTCA
1 -TTTCGCATTGCGATTTTCA
*
44892 -CTCG--TTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
*
44908 TTTCGCATTGCGATTCTCA
1 TTTCGCATTGCGATTTTCA
44927 TTTCGCATTGCGATT
1 TTTCGCATTGCGATT
44942 CTCTCGTTGC
Statistics
Matches: 58, Mismatches: 4, Indels: 11
0.79 0.05 0.15
Matches are distributed among these distances:
14 6 0.10
16 7 0.12
17 3 0.05
18 4 0.07
19 26 0.45
20 12 0.21
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.45
Consensus pattern (19 bp):
TTTCGCATTGCGATTTTCA
Found at i:44948 original size:52 final size:53
Alignment explanation
Indices: 44855--44955 Score: 168
Period size: 52 Copynumber: 1.9 Consensus size: 53
44845 GTGAAATTAG
* *
44855 TTTCGCGTTGCGATTTTCATTTTCGCATTGCGATTCACTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTCTCATTTTCGCATTGCGATTCACTCGTTGCGATTTTCA
*
44908 TTTCGCATTGCGATTCTCA-TTTCGCATTGCGATTCTCTCGTTGCGATT
1 TTTCGCATTGCGATTCTCATTTTCGCATTGCGATTCACTCGTTGCGATT
44956 CTCTCGTTGC
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
52 28 0.62
53 17 0.38
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.45
Consensus pattern (53 bp):
TTTCGCATTGCGATTCTCATTTTCGCATTGCGATTCACTCGTTGCGATTTTCA
Found at i:44953 original size:14 final size:14
Alignment explanation
Indices: 44934--44968 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
44924 TCATTTCGCA
44934 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
44948 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
44962 TTGCGAT
1 TTGCGAT
44969 GGTCATTTCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.43
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:45014 original size:40 final size:40
Alignment explanation
Indices: 44960--45048 Score: 135
Period size: 40 Copynumber: 2.2 Consensus size: 40
44950 GCGATTCTCT
*
44960 CGTTGCGATGGTCATTTCCGCGTTGCGATAGTCA-ATTCTG
1 CGTTGCGATAGTCATTTCCGCGTTGCGATAGTCATATTC-G
* *
45000 CGTTGCGATAGTCATTTTCGTGTTGCGATAGTCATATTCG
1 CGTTGCGATAGTCATTTCCGCGTTGCGATAGTCATATTCG
45040 CGTTGCGAT
1 CGTTGCGAT
45049 TTCCGCGTTG
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
40 41 0.91
41 4 0.09
ACGTcount: A:0.16, C:0.20, G:0.27, T:0.37
Consensus pattern (40 bp):
CGTTGCGATAGTCATTTCCGCGTTGCGATAGTCATATTCG
Found at i:47546 original size:24 final size:24
Alignment explanation
Indices: 47497--47546 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
47487 AAATCCGAGT
** *
47497 ACCAAGATCAAAGTTCGGGTATTG
1 ACCAAGATCAAAGTTCGAATACTG
*
47521 ACCAAGATCAAATTTCGAATACTG
1 ACCAAGATCAAAGTTCGAATACTG
47545 AC
1 AC
47547 TAGTACTCAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.24
Consensus pattern (24 bp):
ACCAAGATCAAAGTTCGAATACTG
Found at i:48462 original size:20 final size:20
Alignment explanation
Indices: 48413--48494 Score: 101
Period size: 20 Copynumber: 4.0 Consensus size: 20
48403 ACAGATTCGA
*
48413 ATTGCGATTTACGTATTCGC
1 ATTGCGATTTACGTAATCGC
48433 ATTGCGATTTACGTAATCGC
1 ATTGCGATTTACGTAATCGC
* **
48453 ATTGCGATTTTCCAAATTCGC
1 ATTGCGATTTACGTAA-TCGC
* *
48474 GTTGCGATTTACGTATTCGC
1 ATTGCGATTTACGTAATCGC
48494 A
1 A
48495 ATATTCGCGT
Statistics
Matches: 51, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
20 36 0.71
21 15 0.29
ACGTcount: A:0.22, C:0.21, G:0.20, T:0.38
Consensus pattern (20 bp):
ATTGCGATTTACGTAATCGC
Found at i:48478 original size:21 final size:21
Alignment explanation
Indices: 48394--48485 Score: 82
Period size: 20 Copynumber: 4.5 Consensus size: 21
48384 CAGAATCTCG
* * *
48394 TTGCGATTCA-CAGATTCGAA
1 TTGCGATTTACCAAATTCGCA
**
48414 TTGCGATTTA-CGTATTCGCA
1 TTGCGATTTACCAAATTCGCA
**
48434 TTGCGATTTACGTAA-TCGCA
1 TTGCGATTTACCAAATTCGCA
* *
48454 TTGCGATTTTCCAAATTCGCG
1 TTGCGATTTACCAAATTCGCA
48475 TTGCGATTTAC
1 TTGCGATTTAC
48486 GTATTCGCAA
Statistics
Matches: 58, Mismatches: 12, Indels: 3
0.79 0.16 0.04
Matches are distributed among these distances:
20 43 0.74
21 15 0.26
ACGTcount: A:0.23, C:0.21, G:0.20, T:0.37
Consensus pattern (21 bp):
TTGCGATTTACCAAATTCGCA
Found at i:48510 original size:29 final size:29
Alignment explanation
Indices: 48468--48523 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
48458 GATTTTCCAA
48468 ATTCGCGTTGCGATTTACGTATTCGCAAT
1 ATTCGCGTTGCGATTTACGTATTCGCAAT
48497 ATTCGCGTTGCGATTTACGTATTCGCA
1 ATTCGCGTTGCGATTTACGTATTCGCA
48524 TTGCGAATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.38
Consensus pattern (29 bp):
ATTCGCGTTGCGATTTACGTATTCGCAAT
Found at i:48550 original size:21 final size:21
Alignment explanation
Indices: 48526--48571 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
48516 TATTCGCATT
48526 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
48547 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
48568 GCGA
1 GCGA
48572 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:49525 original size:29 final size:29
Alignment explanation
Indices: 49483--49550 Score: 136
Period size: 29 Copynumber: 2.3 Consensus size: 29
49473 TAAAATATAA
49483 TTAATAGTCGGGTGATTATTTTGTAACTT
1 TTAATAGTCGGGTGATTATTTTGTAACTT
49512 TTAATAGTCGGGTGATTATTTTGTAACTT
1 TTAATAGTCGGGTGATTATTTTGTAACTT
49541 TTAATAGTCG
1 TTAATAGTCG
49551 AGGGACTCAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.25, C:0.07, G:0.21, T:0.47
Consensus pattern (29 bp):
TTAATAGTCGGGTGATTATTTTGTAACTT
Found at i:52279 original size:40 final size:40
Alignment explanation
Indices: 52230--52320 Score: 146
Period size: 40 Copynumber: 2.3 Consensus size: 40
52220 GAAGAAAAGC
* *
52230 CAAATATCTTTGGGACTATGGCATAATATCATATGAATCT
1 CAAAAATCTTTGGGACTATAGCATAATATCATATGAATCT
52270 CAAAAATCTTTGGGACTATAGCATAATATCATATGAATCT
1 CAAAAATCTTTGGGACTATAGCATAATATCATATGAATCT
* *
52310 CATAAAGCTTT
1 CAAAAATCTTT
52321 CGTTTTACTT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 47 1.00
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.34
Consensus pattern (40 bp):
CAAAAATCTTTGGGACTATAGCATAATATCATATGAATCT
Found at i:52591 original size:15 final size:15
Alignment explanation
Indices: 52567--52596 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
52557 GTATACGCGT
52567 TAAGCCATGATAAAA
1 TAAGCCATGATAAAA
*
52582 TAAGCTATGATAAAA
1 TAAGCCATGATAAAA
52597 GAAAAGCGTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.53, C:0.10, G:0.13, T:0.23
Consensus pattern (15 bp):
TAAGCCATGATAAAA
Found at i:55514 original size:19 final size:17
Alignment explanation
Indices: 55467--55515 Score: 55
Period size: 16 Copynumber: 2.8 Consensus size: 17
55457 TTTAGAAGCA
55467 ATAAAATAAAATAATACG
1 ATAAAA-AAAATAATACG
*
55485 A-GAAAAAAATAATGACG
1 ATAAAAAAAATAAT-ACG
55502 ATAAAACAAAATAA
1 ATAAAA-AAAATAA
55516 AATAAAACTT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 8 0.31
17 7 0.27
18 4 0.15
19 7 0.27
ACGTcount: A:0.69, C:0.06, G:0.08, T:0.16
Consensus pattern (17 bp):
ATAAAAAAAATAATACG
Found at i:56613 original size:3 final size:3
Alignment explanation
Indices: 56605--56651 Score: 85
Period size: 3 Copynumber: 15.3 Consensus size: 3
56595 TTAAAAAATG
56605 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT
56651 A
1 A
56652 TATATATACA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 40 0.93
4 3 0.07
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:56773 original size:72 final size:74
Alignment explanation
Indices: 56663--56941 Score: 216
Period size: 72 Copynumber: 3.7 Consensus size: 74
56653 ATATATACAT
* **
56663 AAATATTTTCAAAAACATATAATATATAAATTTTCAAAATGTTTTTTTTAAACTATATAATATAC
1 AAATATTTTC-AAAAC--ATAATATATAAGTTTTCAAAATGTTTTTTAAAAACTATATAATATAC
*
56728 GAATGTTTTC-A
63 AAATGTTTTCAA
* * * **** *
56739 ACATGTTTTCAAAA-ATATTATATAAGTTTTCAAAAAACGTTTTAAAAACTATATAATATATAAA
1 AAATATTTTCAAAACATAATATATAAGTTTTCAAAATGTTTTTTAAAAACTATATAATATACAAA
56803 TGTTTTCAA
66 TGTTTTCAA
** * * *
56812 AAATATTTTCAAAACTATAATATATGTGTTTTCAAAAATG-TTTTCAAAAATTATAT-ATATA-T
1 AAATATTTTCAAAAC-ATAATATATAAGTTTTC-AAAATGTTTTTTAAAAACTATATAATATACA
56874 AA-GTTTTC-A
64 AATGTTTTCAA
* *
56883 AAATGATTTT-AAAATTTATATATTATATATA-TTTTTAAAATGTTTTTTTAAAAACTATA
1 AAAT-ATTTTCAAAA--CATA-A-TATATA-AGTTTTCAAAATG-TTTTTTAAAAACTATA
56942 CATTATATAT
Statistics
Matches: 162, Mismatches: 29, Indels: 25
0.75 0.13 0.12
Matches are distributed among these distances:
71 9 0.06
72 61 0.38
73 22 0.14
74 14 0.09
75 44 0.27
76 12 0.07
ACGTcount: A:0.45, C:0.06, G:0.05, T:0.44
Consensus pattern (74 bp):
AAATATTTTCAAAACATAATATATAAGTTTTCAAAATGTTTTTTAAAAACTATATAATATACAAA
TGTTTTCAA
Found at i:56842 original size:35 final size:37
Alignment explanation
Indices: 56663--56984 Score: 185
Period size: 37 Copynumber: 8.8 Consensus size: 37
56653 ATATATACAT
**
56663 AAATATTTTCAAAAAC-ATATAATATATAAATTTTC-A
1 AAATATTTTCAAAAACTATAT-ATATATATGTTTTCAA
* *** *
56699 AAATGTTTTTTTTAAACTATATAATATACGAATGTTTTC-A
1 AAAT-ATTTTCAAAAACTATAT-ATATA--TATGTTTTCAA
* *
56739 ACATGTTTTCAAAAA-TAT-TATATA-A-GTTTTCAA
1 AAATATTTTCAAAAACTATATATATATATGTTTTCAA
56772 AAA-ACGTTTT-AAAAACTATATAATATATAAATGTTTTCAA
1 AAATA--TTTTCAAAAACTATAT-ATATAT--ATGTTTTCAA
*
56812 AAATATTTTC-AAAACTATA-ATATATGTGTTTTCAA
1 AAATATTTTCAAAAACTATATATATATATGTTTTCAA
* * *
56847 AAATGTTTTCAAAAATTATATATATATAAGTTTTC-A
1 AAATATTTTCAAAAACTATATATATATATGTTTTCAA
** * *
56883 AAATGATTTT-AAAATTTATATATTATATATATTTTTAA
1 AAAT-ATTTTCAAAAACTATATA-TATATATGTTTTCAA
* * * *
56921 AATGTTTTTTTAAAAACTATACATTATATAT-TTTT-AA
1 AA-ATATTTTCAAAAACTATATA-TATATATGTTTTCAA
56958 AAACTA--TT-AAAAACTATATATTATATA
1 AAA-TATTTTCAAAAACTATATA-TATATA
56985 CGTAGTTTTA
Statistics
Matches: 230, Mismatches: 32, Indels: 50
0.74 0.10 0.16
Matches are distributed among these distances:
32 6 0.03
33 9 0.04
34 25 0.11
35 21 0.09
36 38 0.17
37 46 0.20
38 24 0.10
39 39 0.17
40 21 0.09
41 1 0.00
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (37 bp):
AAATATTTTCAAAAACTATATATATATATGTTTTCAA
Found at i:56855 original size:12 final size:12
Alignment explanation
Indices: 56838--56862 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
56828 ATAATATATG
56838 TGTTTTCAAAAA
1 TGTTTTCAAAAA
56850 TGTTTTCAAAAA
1 TGTTTTCAAAAA
56862 T
1 T
56863 TATATATATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (12 bp):
TGTTTTCAAAAA
Found at i:56932 original size:39 final size:37
Alignment explanation
Indices: 56753--57002 Score: 133
Period size: 39 Copynumber: 6.6 Consensus size: 37
56743 GTTTTCAAAA
* *
56753 ATATTATATA-AGTTTTCAAAAAACG-TTTTAAAAACTAT
1 ATATTATATATA-TTTT--AAAAATGTTTTTAAAAATTAT
* * * * *
56791 ATAATATATAAATGTTTTCAAAAAT-ATTTTCAAAACTAT
1 AT-AT-TATATATATTTT-AAAAATGTTTTTAAAAATTAT
* * *
56830 A-A-TATATGTGTTTTCAAAAATGTTTTCAAAAATTAT
1 ATATTATATATATTTT-AAAAATGTTTTTAAAAATTAT
* * *
56866 ATA-TATATA-AGTTTTCAAAATGATTTTAAAATTTAT
1 ATATTATATATA-TTTTAAAAATGTTTTTAAAAATTAT
* *
56902 ATATTATATATATTTTTAAAATGTTTTTTTAAAAACTAT
1 ATATTATATATATTTTAAAAATG--TTTTTAAAAATTAT
* * * *
56941 ACATTATATAT-TTTTAAAAA--CTATTAAAAACTAT
1 ATATTATATATATTTTAAAAATGTTTTTAAAAATTAT
56975 ATATTATATACGTAGTTTTAAAATATGT
1 ATATTATATA--TA-TTTTAAAA-ATGT
57003 ACATATATAT
Statistics
Matches: 167, Mismatches: 27, Indels: 33
0.74 0.12 0.15
Matches are distributed among these distances:
34 21 0.13
35 17 0.10
36 32 0.19
37 27 0.16
38 19 0.11
39 42 0.25
40 9 0.05
ACGTcount: A:0.45, C:0.06, G:0.05, T:0.45
Consensus pattern (37 bp):
ATATTATATATATTTTAAAAATGTTTTTAAAAATTAT
Found at i:57823 original size:164 final size:163
Alignment explanation
Indices: 57580--58282 Score: 965
Period size: 165 Copynumber: 4.2 Consensus size: 163
57570 ACAATTTTAT
* * * * * * * * *
57580 TGACAAATAGCCCTTCTTGCCTTGAGCTATGTTGTAAATGATATGACCTCGAAGTTGAGTGTAAT
1 TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAAT
* *
57645 CGAACCCAGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTT
66 CGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTT
57710 AGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
131 -GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
*
57744 TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCCTCAAAGCTGAGTGTAAT
1 TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAAT
*
57809 CGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCGT
66 CGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCC-T
* *
57874 TGAGCTAAGCGTAGTCGAACTCAAAGGTCTTTTGG
130 TGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGG
*
57909 TCACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAAT
1 TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAAT
* *
57974 CTAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTT
66 CGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTT
58039 GGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
131 -GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
* * * *
58073 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAA
1 -TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAA
* * * * * *
58138 TCGAACTCGGGGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGT
65 TCGAACTCGGGGGTC-TTTGG---CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGT
* * * **
58203 GCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGG
126 G-CCTTG-AGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
* * * *
58243 TCGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAAT
1 T-GACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAAT
58283 AGTTTGTTTA
Statistics
Matches: 488, Mismatches: 40, Indels: 16
0.90 0.07 0.03
Matches are distributed among these distances:
164 148 0.30
165 229 0.47
166 5 0.01
169 37 0.08
170 69 0.14
ACGTcount: A:0.24, C:0.22, G:0.25, T:0.29
Consensus pattern (163 bp):
TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAAT
CGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTT
GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
Found at i:58170 original size:85 final size:82
Alignment explanation
Indices: 57615--58282 Score: 781
Period size: 85 Copynumber: 8.0 Consensus size: 82
57605 GCTATGTTGT
* * * * * *
57615 AAATGATATGACCTCGAAGTTGAGTGTAATCGAACCCAGGGGTCTTTGG-CAGATAGCCCTTCTC
1 AAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGTCAGATAACCCTTCTC
*
57679 GACTTAAGCTATGCTGC
66 GACTTAAGTTATGCTGC
* * * * **
57696 AAATGATGTGCCTTAG-AGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTC
1 AAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGT--CAGATAACCCTTC
* * *
57760 TAGCCTTGAGTTATGCTGC
64 TCGACTTAAGTTATGCTGC
* *
57779 AAATGATGTGCCCTCAAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGG-CAGATAGCCCTTCTC
1 AAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGTCAGATAACCCTTCTC
57843 GACTTAAGTTATGCTGC
66 GACTTAAGTTATGCTGC
* * * * * ***
57860 AAATGATGTGCCGTTG-AGCTAAGCGTAGTCGAACTCAAAGGTCTTTTGGTCACAGATAACCCTT
1 AAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTC-TTTGGT--CAGATAACCCTT
* * *
57924 CTAGCCTTGAGTTATGCTGC
63 CTCGACTTAAGTTATGCTGC
* *
57944 AAATGATGTGCCCTCGAAGCTGAGTGTAATCTAACTCGGGGGTCTTTGG-CAGATAGCCCTTCTC
1 AAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGTCAGATAACCCTTCTC
* *
58008 GACTTAAGCTATACTGC
66 GACTTAAGTTATGCTGC
* * * * **
58025 AAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTT
1 AAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGG-T--CAGATAACCCTT
58089 CTCGACTTAAGTTATGCTGC
63 CTCGACTTAAGTTATGCTGC
58109 AAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTTGGTCACAGATAACCCTT
1 AAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTC-TTTGGT--CAGATAACCCTT
* * * *
58174 CTAGCCTTGAGTTATGCTGT
63 CTCGACTTAAGTTATGCTGC
58194 AAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGTCGGCAGATAACCCTT
1 AAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGT---CAGATAACCCTT
58259 CTCGACTTAAGTTATGCTGC
63 CTCGACTTAAGTTATGCTGC
58279 AAAT
1 AAAT
58283 AGTTTGTTTA
Statistics
Matches: 488, Mismatches: 83, Indels: 28
0.81 0.14 0.05
Matches are distributed among these distances:
80 77 0.16
81 94 0.19
83 40 0.08
84 120 0.25
85 152 0.31
86 5 0.01
ACGTcount: A:0.24, C:0.22, G:0.26, T:0.29
Consensus pattern (82 bp):
AAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGTCAGATAACCCTTCTC
GACTTAAGTTATGCTGC
Found at i:63711 original size:16 final size:17
Alignment explanation
Indices: 63690--63723 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
63680 GCAATCAAAT
63690 AAAATAAT-ACGAGAAA
1 AAAATAATGACGAGAAA
*
63706 AAAATAATGACGATAAA
1 AAAATAATGACGAGAAA
63723 A
1 A
63724 CAAAATAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.68, C:0.06, G:0.12, T:0.15
Consensus pattern (17 bp):
AAAATAATGACGAGAAA
Found at i:64830 original size:3 final size:3
Alignment explanation
Indices: 64822--64868 Score: 85
Period size: 3 Copynumber: 15.3 Consensus size: 3
64812 TTAAAAAATG
64822 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT
64868 A
1 A
64869 TATATATACA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 40 0.93
4 3 0.07
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:64950 original size:36 final size:35
Alignment explanation
Indices: 64880--65190 Score: 219
Period size: 36 Copynumber: 8.7 Consensus size: 35
64870 ATATATACAT
* **
64880 AAATATTTTCAAAAAC-ATATAATATATAAATTTTCA
1 AAATGTTTT-AAAAACTATATAATATA-ATGTTTTCA
** *
64916 AAATGTTTTTTAAACTATATAATACGAATGTTTTCA
1 AAATGTTTTAAAAACTATATAATA-TAATGTTTTCA
*
64952 ACATGTTTTCAAAAA-TAT-T-ATATAA-GTTTTCAA
1 AAATGTTTT-AAAAACTATATAATATAATGTTTTC-A
*
64985 AAACGTTTTAAAAACTATATAATATAAATGTTTTCA
1 AAATGTTTTAAAAACTATATAATAT-AATGTTTTCA
* * *
65021 AAATATTTTCAAAAC--TATAATATATGTGTTTTCAA
1 AAATGTTTTAAAAACTATATAATATA-ATGTTTTC-A
*
65056 AAATGTTTTCAAAAATTATATATATATAA-GTTTTCA
1 AAATGTTTT-AAAAACTATATA-ATATAATGTTTTCA
* * * *
65092 AAATGATTTTAAAAATTATATATTATATATATTTTTA
1 AAATG-TTTTAAAAACTATATAATATA-ATGTTTTCA
* *
65129 AAATGTTTTTTAAAAACTATACATTAT-ATAGTTTT-A
1 AAATG--TTTTAAAAACTATATAATATAAT-GTTTTCA
** * *
65165 AAAACTATTAAAAACTATATATTATA
1 AAATGTTTTAAAAACTATATAATATA
65191 TACGTAGTGT
Statistics
Matches: 223, Mismatches: 31, Indels: 43
0.75 0.10 0.14
Matches are distributed among these distances:
32 11 0.05
33 14 0.06
34 37 0.17
35 22 0.10
36 78 0.35
37 34 0.15
38 22 0.10
39 5 0.02
ACGTcount: A:0.46, C:0.07, G:0.05, T:0.43
Consensus pattern (35 bp):
AAATGTTTTAAAAACTATATAATATAATGTTTTCA
Found at i:65006 original size:69 final size:68
Alignment explanation
Indices: 64898--65114 Score: 233
Period size: 69 Copynumber: 3.1 Consensus size: 68
64888 TCAAAAACAT
* ** * *
64898 ATAATATATAAATTTTC-AAAATGTTTTTTAAACTATATAATACGAATGTTTTCAACATGTTTTC
1 ATAATATATAAGTTTTCAAAAATGTTTTAAAAACTATATAATA-AAATGTTTTCAAAATGTTTTC
64962 AAAA
65 AAAA
* * *
64966 ATATTATATAAGTTTTCAAAAACGTTTTAAAAACTATATAATATAAATGTTTTCAAAATATTTTC
1 ATAATATATAAGTTTTCAAAAATGTTTTAAAAACTATATAATA-AAATGTTTTCAAAATGTTTTC
65031 AAAA
65 AAAA
** * *
65035 CTATAATATATGTGTTTTCAAAAATGTTTTCAAAAATTATATATATATAA-GTTTTCAAAATGAT
1 --ATAATATATAAGTTTTCAAAAATGTTTT-AAAAACTATATA-ATAAAATGTTTTCAAAATG-T
65099 TTT-AAAA
61 TTTCAAAA
*
65106 ATTATATAT
1 ATAATATAT
65115 TATATATATT
Statistics
Matches: 126, Mismatches: 17, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
68 15 0.12
69 52 0.41
71 39 0.31
72 17 0.13
73 3 0.02
ACGTcount: A:0.45, C:0.07, G:0.06, T:0.43
Consensus pattern (68 bp):
ATAATATATAAGTTTTCAAAAATGTTTTAAAAACTATATAATAAAATGTTTTCAAAATGTTTTCA
AAA
Found at i:65064 original size:12 final size:12
Alignment explanation
Indices: 65047--65071 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
65037 ATAATATATG
65047 TGTTTTCAAAAA
1 TGTTTTCAAAAA
65059 TGTTTTCAAAAA
1 TGTTTTCAAAAA
65071 T
1 T
65072 TATATATATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (12 bp):
TGTTTTCAAAAA
Found at i:68027 original size:3 final size:3
Alignment explanation
Indices: 68019--68082 Score: 71
Period size: 3 Copynumber: 22.0 Consensus size: 3
68009 GTATTTGTAT
**
68019 TAA TAA TAA TAA TAA TACA -AA TAA TAA T-A TAA CGA TAA TAA TAA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
68063 TAA TAA TAA -AA TAA TGA TAA
1 TAA TAA TAA TAA TAA TAA TAA
68083 AAAAAACCCG
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
2 5 0.10
3 45 0.88
4 1 0.02
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:68056 original size:26 final size:26
Alignment explanation
Indices: 68027--68082 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
68017 ATTAATAATA
*
68027 ATAATAATACA-AATAATAATATAACG
1 ATAATAATA-ATAATAATAAAATAACG
*
68053 ATAATAATAATAATAATAAAATAATG
1 ATAATAATAATAATAATAAAATAACG
68079 ATAA
1 ATAA
68083 AAAAAACCCG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
25 1 0.04
26 26 0.96
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.29
Consensus pattern (26 bp):
ATAATAATAATAATAATAAAATAACG
Found at i:68139 original size:4 final size:4
Alignment explanation
Indices: 68125--68158 Score: 50
Period size: 4 Copynumber: 8.5 Consensus size: 4
68115 TAGTTTTAAA
* *
68125 ATAT GTAT ATAT ATAT ATAT ATAT ATAT AAAT AT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT AT
68159 GTATGTACAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (4 bp):
ATAT
Found at i:68139 original size:6 final size:6
Alignment explanation
Indices: 68125--68158 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
68115 TAGTTTTAAA
* *
68125 ATATGT ATATAT ATATAT ATATAT ATATAA ATAT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATAT
68159 GTATGTACAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (6 bp):
ATATAT
Found at i:69788 original size:20 final size:20
Alignment explanation
Indices: 69760--69803 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
69750 CTCTTTTAAT
* *
69760 ATTTTATTTTAAAAATAAAA
1 ATTTAATTTCAAAAATAAAA
* *
69780 ATTTAATTTCATATATAAAA
1 ATTTAATTTCAAAAATAAAA
69800 ATTT
1 ATTT
69804 GTTAAAAACA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (20 bp):
ATTTAATTTCAAAAATAAAA
Found at i:70312 original size:25 final size:25
Alignment explanation
Indices: 70284--70364 Score: 83
Period size: 25 Copynumber: 3.1 Consensus size: 25
70274 GCTGAACTTA
70284 ATTTTATTTATAATATTATTTATTT
1 ATTTTATTTATAATATTATTTATTT
* * * *
70309 ATTTT-TTCAAGGAATATATTTCTTTTTT
1 ATTTTATT-TA-TAATAT-TAT-TTATTT
70337 ATTTTATTTATAATATTATTTATTT
1 ATTTTATTTATAATATTATTTATTT
70362 ATT
1 ATT
70365 CTATATATTA
Statistics
Matches: 43, Mismatches: 8, Indels: 10
0.70 0.13 0.16
Matches are distributed among these distances:
24 2 0.05
25 14 0.33
26 7 0.16
27 7 0.16
28 11 0.26
29 2 0.05
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (25 bp):
ATTTTATTTATAATATTATTTATTT
Found at i:70364 original size:20 final size:21
Alignment explanation
Indices: 70334--70375 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
70324 ATATTTCTTT
70334 TTTATTTTATT-TATAATATTA
1 TTTATTTTATTCTAT-ATATTA
70355 TTTA-TTTATTCTATATATTA
1 TTTATTTTATTCTATATATTA
70375 T
1 T
70376 AGATTAGATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTATTTTATTCTATATATTA
Found at i:72165 original size:16 final size:14
Alignment explanation
Indices: 72105--72166 Score: 52
Period size: 15 Copynumber: 4.2 Consensus size: 14
72095 TTATTATTTC
* *
72105 TAATTTATATATTT
1 TAATTTATAAAATT
*
72119 TTATTTATAAAATT
1 TAATTTATAAAATT
* *
72133 GTAATTCATAGAATT
1 -TAATTTATAAAATT
72148 TATATATTATAAAATT
1 TA-AT-TTATAAAATT
72164 TAA
1 TAA
72167 AACATAAATG
Statistics
Matches: 37, Mismatches: 8, Indels: 5
0.74 0.16 0.10
Matches are distributed among these distances:
14 13 0.35
15 14 0.38
16 10 0.27
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.52
Consensus pattern (14 bp):
TAATTTATAAAATT
Found at i:76843 original size:2 final size:2
Alignment explanation
Indices: 76836--76869 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
76826 ATTCATCTAA
76836 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
76870 TCAATTCATC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:96451 original size:20 final size:20
Alignment explanation
Indices: 96426--96478 Score: 106
Period size: 20 Copynumber: 2.6 Consensus size: 20
96416 ACTGAGGAGT
96426 GTGAGTATCGATACTCTTAG
1 GTGAGTATCGATACTCTTAG
96446 GTGAGTATCGATACTCTTAG
1 GTGAGTATCGATACTCTTAG
96466 GTGAGTATCGATA
1 GTGAGTATCGATA
96479 ACCACATGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.13, G:0.26, T:0.34
Consensus pattern (20 bp):
GTGAGTATCGATACTCTTAG
Found at i:101753 original size:53 final size:53
Alignment explanation
Indices: 101669--101774 Score: 169
Period size: 53 Copynumber: 2.0 Consensus size: 53
101659 TGAGTAAAAT
*
101669 ATGAGATAGAGTAAAGTTAAATGACTAATGGTGTAATTTACCCTT-TTTCCTTC
1 ATGAGATAAAGTAAAGTTAAATGACTAATGGTGTAATTTA-CCTTATTTCCTTC
* *
101722 ATGAGATAAAGTAAAGTTAAATGACTCATGGTGTAATTTAGCTTATTTCCTTC
1 ATGAGATAAAGTAAAGTTAAATGACTAATGGTGTAATTTACCTTATTTCCTTC
101775 TCTTCTCTCT
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
52 3 0.06
53 46 0.94
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (53 bp):
ATGAGATAAAGTAAAGTTAAATGACTAATGGTGTAATTTACCTTATTTCCTTC
Found at i:105640 original size:41 final size:41
Alignment explanation
Indices: 105583--105710 Score: 222
Period size: 41 Copynumber: 3.1 Consensus size: 41
105573 TGTAGTGAGT
105583 TGGATGATGGTGATGTTGAATGAGGGAAAGTAGGGATGGAA
1 TGGATGATGGTGATGTTGAATGAGGGAAAGTAGGGATGGAA
105624 TGGATGATGGTGATGTTGAATGAGGGAAAGTAGGGATGGAA
1 TGGATGATGGTGATGTTGAATGAGGGAAAGTAGGGATGGAA
* *
105665 TGGATGATGGTGATGTTGATTGA-GTAAAGTAGGGATGGAAA
1 TGGATGATGGTGATGTTGAATGAGGGAAAGTAGGGATGG-AA
105706 TGGAT
1 TGGAT
105711 AGTGTCAGAT
Statistics
Matches: 84, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
40 14 0.17
41 70 0.83
ACGTcount: A:0.31, C:0.00, G:0.42, T:0.27
Consensus pattern (41 bp):
TGGATGATGGTGATGTTGAATGAGGGAAAGTAGGGATGGAA
Found at i:107586 original size:23 final size:23
Alignment explanation
Indices: 107532--107587 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
107522 GTTCATGTTC
* ***
107532 GTTCGTTTAACTTTCGTGAACAT
1 GTTCGTTTAACATTCACAAACAT
**
107555 GTTTATTTAACATTCACAAACAT
1 GTTCGTTTAACATTCACAAACAT
107578 GTTCGTTTAA
1 GTTCGTTTAA
107588 TGTTGAGAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.43
Consensus pattern (23 bp):
GTTCGTTTAACATTCACAAACAT
Found at i:113380 original size:29 final size:29
Alignment explanation
Indices: 113348--113440 Score: 87
Period size: 29 Copynumber: 3.1 Consensus size: 29
113338 TTTCAAATTG
*
113348 ATCCTTAAACTTTTAAATATTTTAATTTC
1 ATCCTTAAACTTTTAAATATTTTAATTTA
* * * *
113377 ATCCTTAAACTATGACTATCATTTTAAATTA
1 ATCCTTAAACTTTTA-AAT-ATTTTAATTTA
* * * *
113408 ATCCTCAAACTTTTGAATATTTCAATTTT
1 ATCCTTAAACTTTTAAATATTTTAATTTA
113437 ATCC
1 ATCC
113441 CCAAACTATG
Statistics
Matches: 49, Mismatches: 13, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
29 25 0.51
30 4 0.08
31 20 0.41
ACGTcount: A:0.34, C:0.17, G:0.02, T:0.46
Consensus pattern (29 bp):
ATCCTTAAACTTTTAAATATTTTAATTTA
Found at i:113418 original size:60 final size:60
Alignment explanation
Indices: 113337--113452 Score: 160
Period size: 60 Copynumber: 1.9 Consensus size: 60
113327 TGTGACTCTA
* * * **
113337 ATTTCAAATTGATCCTTAAACTTTTAAATATTTTAATTTCATCCTTAAACTATGACTATC
1 ATTTCAAATTAATCCTCAAACTTTTAAATATTTCAATTTCATCCCCAAACTATGACTATC
* * *
113397 ATTTTAAATTAATCCTCAAACTTTTGAATATTTCAATTTTATCCCCAAACTATGAC
1 ATTTCAAATTAATCCTCAAACTTTTAAATATTTCAATTTCATCCCCAAACTATGAC
113453 CTTAATTCTA
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
60 48 1.00
ACGTcount: A:0.35, C:0.18, G:0.03, T:0.43
Consensus pattern (60 bp):
ATTTCAAATTAATCCTCAAACTTTTAAATATTTCAATTTCATCCCCAAACTATGACTATC
Found at i:113465 original size:60 final size:59
Alignment explanation
Indices: 113329--113485 Score: 156
Period size: 60 Copynumber: 2.6 Consensus size: 59
113319 CTTAAAAGTG
* * * * **
113329 TGACTCTAATT-TCAAATTGATCCTTAAACTTTTAAATATTTTAATTTCATCCTTAAACTA
1 TGACTATAATTCT-AAATTAATCC-TAAACTTTTGAATATTTCAATTTCATCCCCAAACTA
* * *
113389 TGACTATCATTTTAAATTAATCCTCAAACTTTTGAATATTTCAATTTTATCCCCAAACTA
1 TGACTATAATTCTAAATTAATCCT-AAACTTTTGAATATTTCAATTTCATCCCCAAACTA
*
113449 TGACCT-TAATTCTAAATTAGTCCATAAACCTTTTGAA
1 TGA-CTATAATTCTAAATTAATCC-TAAA-CTTTTGAA
113486 CTTAAAAACT
Statistics
Matches: 81, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
59 1 0.01
60 68 0.84
61 12 0.15
ACGTcount: A:0.35, C:0.18, G:0.04, T:0.42
Consensus pattern (59 bp):
TGACTATAATTCTAAATTAATCCTAAACTTTTGAATATTTCAATTTCATCCCCAAACTA
Found at i:114163 original size:60 final size:59
Alignment explanation
Indices: 114019--114177 Score: 151
Period size: 60 Copynumber: 2.6 Consensus size: 59
114009 AAACTGAAAG
** * *
114019 ATTCAAAAGTTT-AGAGACCAATTTAGAATGAGGGTCATAGCATGGAGATGAAATTGGAAT
1 ATTCAAAAGTTTAAG-GA-CAATTTAGAATGAAAGTCATAGCATGGAGATAAAATTAGAAT
* * * * ** *
114079 GTTCAAAATTTTAAGGACTGATTTAGAGTGAAAGTCATAGTTTGGGGATAAAATTAGAAT
1 ATTCAAAAGTTTAAGGAC-AATTTAGAATGAAAGTCATAGCATGGAGATAAAATTAGAAT
*
114139 ATTCAAAAGTTTAAGGATCAATTTA-AATAAAAAGTCATA
1 ATTCAAAAGTTTAAGGA-CAATTTAGAAT-GAAAGTCATA
114178 ATTTGAGGAT
Statistics
Matches: 79, Mismatches: 16, Indels: 8
0.77 0.16 0.08
Matches are distributed among these distances:
59 3 0.04
60 73 0.92
61 3 0.04
ACGTcount: A:0.42, C:0.07, G:0.21, T:0.30
Consensus pattern (59 bp):
ATTCAAAAGTTTAAGGACAATTTAGAATGAAAGTCATAGCATGGAGATAAAATTAGAAT
Found at i:117486 original size:134 final size:134
Alignment explanation
Indices: 117236--117503 Score: 419
Period size: 134 Copynumber: 2.0 Consensus size: 134
117226 GTAATGTACC
* * *
117236 AAGTATTTCGTGATAAAATTTGATAACTCTCGTCATCCAAAATCTATCTGAAATGTGCTGCAATC
1 AAGTATTTCATGATAAAATTCGATAACTCTCCTCATCCAAAATCTATCTGAAATGTGCTGCAATC
* * * * * *
117301 TCTTAATATGCATAAAAGTGTAGGCTGTAATATCAAATAAACACAACCATAGATAACGAATCATT
66 TCTTAACATGCACAAAAGTGTAGGCCGCAATATCAAATAAACACAACCATAGATAACGAACCATA
117366 ATCA
131 ATCA
* *
117370 AAGTCTTTCATGATAAAATTCGATAACTCTCCTCATCCTAAATCTATCTGAAATGTGCTGCAATC
1 AAGTATTTCATGATAAAATTCGATAACTCTCCTCATCCAAAATCTATCTGAAATGTGCTGCAATC
* *
117435 TCTTAACATGCACAAAAGTGTAGGCCGCAATATCGAATAAACACAGCCATAGATAACGAACCATA
66 TCTTAACATGCACAAAAGTGTAGGCCGCAATATCAAATAAACACAACCATAGATAACGAACCATA
117500 ATCA
131 ATCA
117504 CTACGGAGAT
Statistics
Matches: 121, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
134 121 1.00
ACGTcount: A:0.39, C:0.20, G:0.13, T:0.28
Consensus pattern (134 bp):
AAGTATTTCATGATAAAATTCGATAACTCTCCTCATCCAAAATCTATCTGAAATGTGCTGCAATC
TCTTAACATGCACAAAAGTGTAGGCCGCAATATCAAATAAACACAACCATAGATAACGAACCATA
ATCA
Found at i:119149 original size:14 final size:14
Alignment explanation
Indices: 119130--119159 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
119120 TTCAGGTAAA
*
119130 ATTATTTTTTTTAT
1 ATTATTTATTTTAT
119144 ATTATTTATTTTAT
1 ATTATTTATTTTAT
119158 AT
1 AT
119160 GGGGTATTTA
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:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (14 bp):
ATTATTTATTTTAT
Found at i:122862 original size:18 final size:18
Alignment explanation
Indices: 122839--122902 Score: 105
Period size: 18 Copynumber: 3.7 Consensus size: 18
122829 ATGAAGAAGA
122839 AATTAGAATCTGTAAAGG
1 AATTAGAATCTGTAAAGG
122857 AATTAGAATCTGTAAAGG
1 AATTAGAATCTGTAAAGG
122875 AATTAGAATCTGT--AGG
1 AATTAGAATCTGTAAAGG
*
122891 AATTGGAATCTG
1 AATTAGAATCTG
122903 AATCTGAAAT
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
16 14 0.31
18 31 0.69
ACGTcount: A:0.41, C:0.06, G:0.23, T:0.30
Consensus pattern (18 bp):
AATTAGAATCTGTAAAGG
Found at i:123549 original size:33 final size:33
Alignment explanation
Indices: 123489--123558 Score: 106
Period size: 32 Copynumber: 2.1 Consensus size: 33
123479 CTAAACTCGA
*
123489 ACCCGACCCGAATATCACACTTAAAAAAAACCCG
1 ACCCGACCCGAATATCAAACTT-AAAAAAACCCG
*
123523 ACCCGACCCG-ATATTAAACTTAAAAAAACCCG
1 ACCCGACCCGAATATCAAACTTAAAAAAACCCG
123555 ACCC
1 ACCC
123559 AACCTGAACT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 15 0.44
33 9 0.26
34 10 0.29
ACGTcount: A:0.43, C:0.36, G:0.09, T:0.13
Consensus pattern (33 bp):
ACCCGACCCGAATATCAAACTTAAAAAAACCCG
Found at i:123630 original size:28 final size:27
Alignment explanation
Indices: 123581--123636 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 27
123571 AATTTAATTT
*
123581 TTTTTAAAAAAAATCCAACCGATCCCGAA
1 TTTTTAAAAAAAA-CAAACCGA-CCCGAA
123610 TTTTTAAAAAAAA-AAATCCGACCCGAA
1 TTTTTAAAAAAAACAAA-CCGACCCGAA
123637 ACATCAAAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
27 8 0.32
28 4 0.16
29 13 0.52
ACGTcount: A:0.48, C:0.21, G:0.07, T:0.23
Consensus pattern (27 bp):
TTTTTAAAAAAAACAAACCGACCCGAA
Done.