Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007391.1 Hibiscus syriacus cultivar Beakdansim tig00019905_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: 119655
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:7258 original size:30 final size:31
Alignment explanation
Indices: 7199--7259 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
7189 AATAGATGGT
*
7199 TTTGGAAGCTTTAGAAAGTTATTTGGACCAA
1 TTTGGAAGCTTTAGAAAGTTATATGGACCAA
*
7230 TTTGGAAGCTTATAG-AGGTT-TATGGACCAA
1 TTTGGAAGCTT-TAGAAAGTTATATGGACCAA
7260 AAACGTAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
30 9 0.33
31 15 0.56
32 3 0.11
ACGTcount: A:0.31, C:0.10, G:0.25, T:0.34
Consensus pattern (31 bp):
TTTGGAAGCTTTAGAAAGTTATATGGACCAA
Found at i:13888 original size:31 final size:29
Alignment explanation
Indices: 13828--13897 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 29
13818 AATTTTTAAC
**
13828 TAGTGACCAAAATATAATTTTTAAAAGTT
1 TAGTGACCAAAATATAATTTGGAAAAGTT
*
13857 TAGTGACCAAAGTATAAACTTTGGAAAAGTT
1 TAGTGACCAAAATAT-AA-TTTGGAAAAGTT
13888 TAAG-GACCAA
1 T-AGTGACCAA
13898 TGTGTAATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 14 0.40
30 2 0.06
31 17 0.49
32 2 0.06
ACGTcount: A:0.44, C:0.10, G:0.16, T:0.30
Consensus pattern (29 bp):
TAGTGACCAAAATATAATTTGGAAAAGTT
Found at i:16147 original size:25 final size:25
Alignment explanation
Indices: 16118--16166 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
16108 TGATGTACAT
* *
16118 TCTACGCGGTACTTTCGAGTGCAAC
1 TCTACACGGCACTTTCGAGTGCAAC
16143 TCTACACGGCACTTTCGAGTGCAA
1 TCTACACGGCACTTTCGAGTGCAA
16167 TTATATGTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.22, C:0.29, G:0.22, T:0.27
Consensus pattern (25 bp):
TCTACACGGCACTTTCGAGTGCAAC
Found at i:16191 original size:24 final size:24
Alignment explanation
Indices: 16161--16213 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
16151 GCACTTTCGA
*
16161 GTGCAATTATATGTGACACT-TTAT
1 GTGCAATTATACGTGACACTATT-T
*
16185 GTGCAATTCTACGTGACACTATTT
1 GTGCAATTATACGTGACACTATTT
16209 GTGCA
1 GTGCA
16214 TTCAAGAAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 24 0.92
25 2 0.08
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.38
Consensus pattern (24 bp):
GTGCAATTATACGTGACACTATTT
Found at i:19127 original size:16 final size:18
Alignment explanation
Indices: 19096--19128 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
19086 TTTACAGGCT
19096 AAAATATATAACTTTTAA
1 AAAATATATAACTTTTAA
19114 AAAAT-TATAA-TTTTA
1 AAAATATATAACTTTTA
19129 GTCCCTAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 5 0.33
18 5 0.33
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (18 bp):
AAAATATATAACTTTTAA
Found at i:19187 original size:29 final size:29
Alignment explanation
Indices: 19105--19194 Score: 85
Period size: 29 Copynumber: 3.0 Consensus size: 29
19095 TAAAATATAT
*
19105 AACTTTTAAAAAATTATAATTTTAGTCC-CTA
1 AACTTTT-CAAAATT-TAATTTTAG-CCACTA
* *
19136 AACTTTTCAAAGTTTATACTTTAGCCACTA
1 AACTTTTCAAAATTTA-ATTTTAGCCACTA
*
19166 AAC-TTTCAAAATTTACATTTTAGTCACTA
1 AACTTTTCAAAATTTA-ATTTTAGCCACTA
19195 GAAAAAATTT
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
29 26 0.52
30 17 0.34
31 7 0.14
ACGTcount: A:0.38, C:0.17, G:0.04, T:0.41
Consensus pattern (29 bp):
AACTTTTCAAAATTTAATTTTAGCCACTA
Found at i:26564 original size:29 final size:30
Alignment explanation
Indices: 26512--26576 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 30
26502 ATTTTTGTCC
** * *
26512 CTAAACTTTTCAAAGTTTATACTTTGGCCA
1 CTAAACTTTTCAAAACTTACACTTTAGCCA
*
26542 CTAAAC-TTTCAAAACTTACACTTTAGTCA
1 CTAAACTTTTCAAAACTTACACTTTAGCCA
26571 CTAAAC
1 CTAAAC
26577 AAAATTTGTG
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 24 0.80
30 6 0.20
ACGTcount: A:0.35, C:0.23, G:0.06, T:0.35
Consensus pattern (30 bp):
CTAAACTTTTCAAAACTTACACTTTAGCCA
Found at i:29936 original size:20 final size:20
Alignment explanation
Indices: 29898--29937 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
29888 CATTTAAATG
* * *
29898 GTAAACGAACATAACCGAAC
1 GTAAACAAACACAAACGAAC
29918 GTAAACAAACACAAACGAAC
1 GTAAACAAACACAAACGAAC
29938 TAACATAAAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.55, C:0.25, G:0.12, T:0.07
Consensus pattern (20 bp):
GTAAACAAACACAAACGAAC
Found at i:30256 original size:14 final size:14
Alignment explanation
Indices: 30234--30269 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
30224 GCCCTCTGTT
*
30234 TGAATATAAATGAA
1 TGAACATAAATGAA
30248 TGAACATAAATGAA
1 TGAACATAAATGAA
*
30262 CGAACATA
1 TGAACATA
30270 TAATTGAACG
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:0.56, C:0.08, G:0.14, T:0.22
Consensus pattern (14 bp):
TGAACATAAATGAA
Found at i:30277 original size:16 final size:15
Alignment explanation
Indices: 30237--30279 Score: 52
Period size: 14 Copynumber: 2.8 Consensus size: 15
30227 CTCTGTTTGA
*
30237 ATATAAATGAATGAAC
1 ATAT-AATGAACGAAC
30253 ATA-AATGAACGAAC
1 ATATAATGAACGAAC
30267 ATATAATTGAACG
1 ATATAA-TGAACG
30280 TTCACGAACG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
14 13 0.54
15 2 0.08
16 9 0.38
ACGTcount: A:0.53, C:0.09, G:0.14, T:0.23
Consensus pattern (15 bp):
ATATAATGAACGAAC
Found at i:30787 original size:16 final size:15
Alignment explanation
Indices: 30762--30791 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
30752 AATTAGTAAT
30762 TTAGAAGTTAGTGGA
1 TTAGAAGTTAGTGGA
30777 TTAGTAAGTTAGTGG
1 TTAG-AAGTTAGTGG
30792 TTAAGAGTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.30, C:0.00, G:0.33, T:0.37
Consensus pattern (15 bp):
TTAGAAGTTAGTGGA
Found at i:31002 original size:19 final size:18
Alignment explanation
Indices: 30967--31010 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
30957 ACATTAAACT
30967 TATATTAAATATATATTA
1 TATATTAAATATATATTA
*
30985 TATATTATAATA-ATTATTT
1 TATATTA-AATATA-TATTA
31004 TATATTA
1 TATATTA
31011 CATGTTGTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TATATTAAATATATATTA
Found at i:32238 original size:2 final size:2
Alignment explanation
Indices: 32231--32263 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
32221 TTATATCTTT
32231 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
32264 TTCTGTTTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:32501 original size:13 final size:14
Alignment explanation
Indices: 32476--32518 Score: 54
Period size: 13 Copynumber: 3.2 Consensus size: 14
32466 TCTATGTATT
*
32476 TTTAT-TTTATTTA
1 TTTATGTTTCTTTA
32489 TTTATG-TTCTTTA
1 TTTATGTTTCTTTA
*
32502 TTTTTGTTTCTTTA
1 TTTATGTTTCTTTA
32516 TTT
1 TTT
32519 TCATTTTGCT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
13 16 0.62
14 10 0.38
ACGTcount: A:0.14, C:0.05, G:0.05, T:0.77
Consensus pattern (14 bp):
TTTATGTTTCTTTA
Found at i:32514 original size:14 final size:13
Alignment explanation
Indices: 32485--32519 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
32475 TTTTATTTTA
*
32485 TTTATTTATGTTC
1 TTTATTTTTGTTC
32498 TTTATTTTTGTTTC
1 TTTATTTTTG-TTC
32512 TTTATTTT
1 TTTATTTT
32520 CATTTTGCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 9 0.45
14 11 0.55
ACGTcount: A:0.11, C:0.06, G:0.06, T:0.77
Consensus pattern (13 bp):
TTTATTTTTGTTC
Found at i:36407 original size:21 final size:21
Alignment explanation
Indices: 36374--36413 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
36364 GCAAAGAAGA
*
36374 TGGAAGAGAAGATTAAGATAC
1 TGGAAGAGAAGATGAAGATAC
**
36395 TGGAAGATCAGATGAAGAT
1 TGGAAGAGAAGATGAAGAT
36414 GGTCAAAGGG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.45, C:0.05, G:0.30, T:0.20
Consensus pattern (21 bp):
TGGAAGAGAAGATGAAGATAC
Found at i:38373 original size:19 final size:18
Alignment explanation
Indices: 38338--38381 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
38328 ATATTAAACT
38338 TATATTAAATATATATTA
1 TATATTAAATATATATTA
*
38356 TATATTATAATA-ATTATTT
1 TATATTA-AATATA-TATTA
38375 TATATTA
1 TATATTA
38382 CATGTTGCAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TATATTAAATATATATTA
Found at i:39440 original size:18 final size:19
Alignment explanation
Indices: 39417--39459 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
39407 AATTTGACCC
39417 TTATATTATTT-TTTTATT
1 TTATATTATTTATTTTATT
39435 TTATATTATTTATTTTATT
1 TTATATTATTTATTTTATT
*
39454 GTATAT
1 TTATAT
39460 ACATATATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 11 0.48
19 12 0.52
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (19 bp):
TTATATTATTTATTTTATT
Found at i:39467 original size:2 final size:2
Alignment explanation
Indices: 39455--39497 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
39445 TATTTTATTG
*
39455 TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
39497 T
1 T
39498 TAATATTTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:39597 original size:2 final size:2
Alignment explanation
Indices: 39590--39616 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
39580 ATCTTATAAT
39590 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
39617 TTATTATTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:39639 original size:14 final size:15
Alignment explanation
Indices: 39565--39642 Score: 52
Period size: 16 Copynumber: 5.1 Consensus size: 15
39555 TGGTTATTTC
39565 TTATTTAATTATTATAT
1 TTATTT-ATTATT-TAT
* *
39582 CTTA-TAATTATATAT
1 -TTATTTATTATTTAT
* * *
39597 ATATATATATATATAT
1 TTATTTAT-TATTTAT
*
39613 ATATTTATTATTTAT
1 TTATTTATTATTTAT
39628 TTATTT-TTATTTAT
1 TTATTTATTATTTAT
39642 T
1 T
39643 ACTATTATAT
Statistics
Matches: 50, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
14 11 0.22
15 16 0.32
16 19 0.38
17 1 0.02
18 3 0.06
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (15 bp):
TTATTTATTATTTAT
Found at i:39648 original size:10 final size:10
Alignment explanation
Indices: 39558--39667 Score: 53
Period size: 11 Copynumber: 10.2 Consensus size: 10
39548 TTTTGTTTGG
*
39558 TTATTTCTTA
1 TTATTTATTA
*
39568 TTTAATTATTA
1 -TTATTTATTA
*
39579 -TATCTTATAA
1 TTAT-TTATTA
*
39589 TTATATATATA
1 TTATTTAT-TA
*
39600 TATATATATATA
1 T-TATTTAT-TA
39612 TATATTTATTA
1 T-TATTTATTA
*
39623 TTTATTTATTT
1 -TTATTTATTA
39634 TTATTTATTA
1 TTATTTATTA
*
39644 CTATTATATCATA
1 TTATT-TAT--TA
39657 TTATTT-TTA
1 TTATTTATTA
39666 TT
1 TT
39668 TTCTAGTTTT
Statistics
Matches: 80, Mismatches: 11, Indels: 18
0.73 0.10 0.17
Matches are distributed among these distances:
9 6 0.08
10 21 0.26
11 27 0.34
12 20 0.25
13 6 0.08
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.63
Consensus pattern (10 bp):
TTATTTATTA
Found at i:39688 original size:37 final size:35
Alignment explanation
Indices: 39612--39721 Score: 107
Period size: 37 Copynumber: 3.0 Consensus size: 35
39602 TATATATATA
* *
39612 TATATTTATTATTTATTTATTTTTATTTATTA-CTAT
1 TATATATATTA-TT-TTTATTTTTATTTTTTACCTAT
39648 TATATCATATTATTTTTATTTTCTAGTTTTTTACCT-T
1 TATAT-ATATTATTTTTATTTT-TA-TTTTTTACCTAT
* *
39685 TATATATATACATTATTATTTTATATTTTTTACCTAT
1 TATATATAT-TATTTTTATTTT-TATTTTTTACCTAT
39722 ACTATTTATT
Statistics
Matches: 63, Mismatches: 5, Indels: 11
0.80 0.06 0.14
Matches are distributed among these distances:
35 8 0.13
36 23 0.37
37 30 0.48
38 2 0.03
ACGTcount: A:0.27, C:0.07, G:0.01, T:0.65
Consensus pattern (35 bp):
TATATATATTATTTTTATTTTTATTTTTTACCTAT
Found at i:43788 original size:3 final size:3
Alignment explanation
Indices: 43780--43805 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
43770 TATTGAAATT
43780 AGA AGA AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AG
43806 TAATTTAGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:44848 original size:11 final size:11
Alignment explanation
Indices: 44832--44881 Score: 73
Period size: 11 Copynumber: 4.5 Consensus size: 11
44822 CTATGTAGTG
*
44832 TATATATGAAC
1 TATATATAAAC
44843 TATATATAAAC
1 TATATATAAAC
*
44854 TATATTATATAC
1 TATA-TATAAAC
44866 TATATATAAAC
1 TATATATAAAC
44877 TATAT
1 TATAT
44882 GATTTATTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
11 25 0.71
12 10 0.29
ACGTcount: A:0.48, C:0.08, G:0.02, T:0.42
Consensus pattern (11 bp):
TATATATAAAC
Found at i:44870 original size:95 final size:93
Alignment explanation
Indices: 44748--44918 Score: 238
Period size: 95 Copynumber: 1.8 Consensus size: 93
44738 TATATATATA
* * * *
44748 TATATATATATATATATATATAATATATATAAACTATATGGTTTA-TATTTATAATTTTATATAT
1 TATATATAAATATATATATATAATATATATAAACTATATGATTTATTA-ATATAA-ATTATATA-
*
44812 TGTATATAAACTATGTAGTGTATATATGAAC
63 TATATATAAACTATGTAGTGTATATATGAAC
*
44843 TATATATAAACTATAT-TATATACTATATATAAACTATATGATTTATTAATATAAATTATATATA
1 TATATATAAA-TATATATATATAATATATATAAACTATATGATTTATTAATATAAATTATATATA
44907 TATATAAACTAT
65 TATATAAACTAT
44919 AAAGTATATA
Statistics
Matches: 68, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
93 13 0.19
94 7 0.10
95 41 0.60
96 7 0.10
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.46
Consensus pattern (93 bp):
TATATATAAATATATATATATAATATATATAAACTATATGATTTATTAATATAAATTATATATAT
ATATAAACTATGTAGTGTATATATGAAC
Found at i:44928 original size:2 final size:2
Alignment explanation
Indices: 44723--44912 Score: 103
Period size: 2 Copynumber: 95.0 Consensus size: 2
44713 TTTAAACAAT
44723 TA TA TA TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
44764 TA TA TA -A TA TA TA TA AA CTA TA TGG TT TA TA TT TA TA -A T- TT
1 TA TA TA TA TA TA TA TA TA -TA TA T-A TA TA TA TA TA TA TA TA TA
* * * *
44805 TA TA TA T- TG TA TA TA AA CTA TG TA GTG TA TA TA TGA -A CTA TA
1 TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA T-A TA -TA TA
* * *
44847 TA TA AA CTA TA T- TA TA TA CTA TA TA TA AA CTA TA TGA TT TA T-
1 TA TA TA -TA TA TA TA TA TA -TA TA TA TA TA -TA TA T-A TA TA TA
*
44889 TA -A TA TA AA T- TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
44913 AACTATAAAG
Statistics
Matches: 145, Mismatches: 23, Indels: 40
0.70 0.11 0.19
Matches are distributed among these distances:
1 10 0.07
2 123 0.85
3 12 0.08
ACGTcount: A:0.45, C:0.03, G:0.04, T:0.47
Consensus pattern (2 bp):
TA
Found at i:44985 original size:134 final size:130
Alignment explanation
Indices: 44723--44992 Score: 284
Period size: 134 Copynumber: 2.0 Consensus size: 130
44713 TTTAAACAAT
* * * *
44723 TATA-TATATATTATATATATATATATATATATATATATATATATATAATATATATAAACTATAT
1 TATATTATATACTATATATAAATATATATATATATATAAATATATATAATATATATAAACTATAA
* * * * *
44787 GGTTTATATTTATAATTTTATATATTGTATATAAACTATGTAGTGTATATATGAACTATATATAA
66 AGTATATATTTATAACTTTATATAATGTATATAAACTATATAGTGTATATATG-A-TATATATAA
44852 AC
129 AC
*
44854 TATATTATATACTATATATAAACTATATGATTTATTAATATAAAT-TATAT-ATATATATAAACT
1 TATATTATATACTATATATAAA-TATAT-ATATA-T-ATATAAATATATATAATATATATAAACT
44917 ATAAAGTATATAGTTTATATACTTTATATAATGATATTAATAAACTATATAGT-TCAT-TA-G-T
62 ATAAAGTATATA-TTTATA-ACTTTATATAATG-TA-T-ATAAACTATATAGTGT-ATATATGAT
*
44978 ATGTATAAAC
121 ATATATAAAC
44988 TATAT
1 TATAT
44993 ATTAATTTAT
Statistics
Matches: 117, Mismatches: 11, Indels: 19
0.80 0.07 0.13
Matches are distributed among these distances:
131 4 0.03
132 15 0.13
133 5 0.04
134 41 0.35
135 12 0.10
136 18 0.15
137 3 0.03
138 4 0.03
139 15 0.13
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.46
Consensus pattern (130 bp):
TATATTATATACTATATATAAATATATATATATATATAAATATATATAATATATATAAACTATAA
AGTATATATTTATAACTTTATATAATGTATATAAACTATATAGTGTATATATGATATATATAAAC
Found at i:45293 original size:18 final size:18
Alignment explanation
Indices: 45270--45313 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
45260 CATTTTGTGA
* *
45270 TTTCTCTCTCTCTCTCTC
1 TTTCTCTCTCTCCCCCTC
*
45288 TTTCTCTTTCTCCCCCTC
1 TTTCTCTCTCTCCCCCTC
*
45306 TTACTCTC
1 TTTCTCTC
45314 CGTTTCTCTT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.02, C:0.45, G:0.00, T:0.52
Consensus pattern (18 bp):
TTTCTCTCTCTCCCCCTC
Found at i:45376 original size:21 final size:21
Alignment explanation
Indices: 45350--45405 Score: 112
Period size: 21 Copynumber: 2.7 Consensus size: 21
45340 TCTCTAGAAA
45350 TTCATTCGTGTTCAACATTTG
1 TTCATTCGTGTTCAACATTTG
45371 TTCATTCGTGTTCAACATTTG
1 TTCATTCGTGTTCAACATTTG
45392 TTCATTCGTGTTCA
1 TTCATTCGTGTTCA
45406 TATCAAAAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.18, C:0.20, G:0.14, T:0.48
Consensus pattern (21 bp):
TTCATTCGTGTTCAACATTTG
Found at i:45564 original size:101 final size:102
Alignment explanation
Indices: 45389--45588 Score: 262
Period size: 101 Copynumber: 2.0 Consensus size: 102
45379 TGTTCAACAT
* * * * *
45389 TTGTTCATTCGTGTTCATATCAAAAACCTCCTTTGATCTTCACAAGCACCAAAACCCAAATCATT
1 TTGTTCATTCGTGTTCATACCAAAAACCTCATTTGATCTTCAAAAACACCAAAACCCAAACCATT
* *
45454 TCCCGTTTTTT-ATCAAACACC-CAAAATTTAAACCG
66 TCCCATTTTTTCATCAAACACCTAAAAATTTAAACCG
* *
45489 TTGTTCATTCGTGTTTATCCCAAAAACCCTCATTTGATCTTCAAAAACACCAAAACCCAAACCCA
1 TTGTTCATTCGTGTTCATACCAAAAA-CCTCATTTGATCTTCAAAAACACCAAAACCCAAA-CCA
*
45554 -TTCCTATTTTTTCGATCAAACACCTAAAAATTTAA
64 TTTCCCATTTTTTC-ATCAAACACCTAAAAATTTAA
45589 CCCTTTTCCA
Statistics
Matches: 85, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
100 23 0.27
101 41 0.48
102 2 0.02
103 10 0.12
104 9 0.11
ACGTcount: A:0.34, C:0.28, G:0.06, T:0.32
Consensus pattern (102 bp):
TTGTTCATTCGTGTTCATACCAAAAACCTCATTTGATCTTCAAAAACACCAAAACCCAAACCATT
TCCCATTTTTTCATCAAACACCTAAAAATTTAAACCG
Found at i:45877 original size:53 final size:52
Alignment explanation
Indices: 45778--46017 Score: 176
Period size: 53 Copynumber: 4.5 Consensus size: 52
45768 CTTCACTTTT
* * * * * *
45778 TATCTCTGTTCATATTCTCTAATCCC-AAACCCTAACCTAACCTCTTCATCTTT
1 TATCTCTGTTCATCTTCTCTAA-CCCTAAACCC-AAACGAGCATCTTCATCTTC
* * * *
45831 TGTTTTTGTTCATCTTCTCTAACCCTAAACCCAAATCGAGTATCTTCATCTTC
1 TATCTCTGTTCATCTTCTCTAACCCTAAACCCAAA-CGAGCATCTTCATCTTC
* * * * ** * * *
45884 TATCTCTATTCATATTTTCTAACCTTAAACTAAAACCAAACCTCTTCATCTTC
1 TATCTCTGTTCATCTTCTCTAACCCTAAACCCAAA-CGAGCATCTTCATCTTC
* * * * * *
45937 TATATCTGTTTATCTTCTTTAACCCTAAACCCAAACTGAGCATTTTTATCTTT
1 TATCTCTGTTCATCTTCTCTAACCCTAAACCCAAAC-GAGCATCTTCATCTTC
** *
45990 TGCCTCTGTTTATCTTCTCTAACCCTAA
1 TATCTCTGTTCATCTTCTCTAACCCTAA
46018 CACTTATTAT
Statistics
Matches: 141, Mismatches: 43, Indels: 6
0.74 0.23 0.03
Matches are distributed among these distances:
52 6 0.04
53 135 0.96
ACGTcount: A:0.25, C:0.29, G:0.04, T:0.42
Consensus pattern (52 bp):
TATCTCTGTTCATCTTCTCTAACCCTAAACCCAAACGAGCATCTTCATCTTC
Found at i:46011 original size:106 final size:106
Alignment explanation
Indices: 45811--46013 Score: 237
Period size: 106 Copynumber: 1.9 Consensus size: 106
45801 CCCAAACCCT
* * * * * *
45811 AACCTAACCTCTTCATCTTTTGTTTTTGTTCATCTTCTCTAACCCTAAACCCAAATCGAGTATCT
1 AACCAAACCTCTTCATCTTCTATATCTGTTCATCTTCTCTAACCCTAAACCCAAATCGAGCATCT
* *
45876 TCATCTTCTATCTCTATTCATATTTTCTAACCTTAAACTAA
66 TCATCTTCTACCTCTATTCATATTCTCTAACCTTAAACTAA
* * *
45917 AACCAAACCTCTTCATCTTCTATATCTGTTTATCTTCTTTAACCCTAAACCCAAA-CTGAGCATT
1 AACCAAACCTCTTCATCTTCTATATCTGTTCATCTTCTCTAACCCTAAACCCAAATC-GAGCATC
* * * * * *
45981 TTTATCTTTTGCCTCTGTTTATCTTCTCTAACC
65 TTCATCTTCTACCTCTATTCATATTCTCTAACC
46014 CTAACACTTA
Statistics
Matches: 79, Mismatches: 17, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
105 1 0.01
106 78 0.99
ACGTcount: A:0.25, C:0.28, G:0.04, T:0.42
Consensus pattern (106 bp):
AACCAAACCTCTTCATCTTCTATATCTGTTCATCTTCTCTAACCCTAAACCCAAATCGAGCATCT
TCATCTTCTACCTCTATTCATATTCTCTAACCTTAAACTAA
Found at i:46113 original size:55 final size:52
Alignment explanation
Indices: 46001--46123 Score: 149
Period size: 52 Copynumber: 2.3 Consensus size: 52
45991 GCCTCTGTTT
* *
46001 ATCTTCTCTAACCCTAACACTTATTATTCACCATCTTCTTCTTCTTTTGTAC
1 ATCTTCTCTAACCCTAACACATATTATTCACCATCTTCTTCCTCTTTTGTAC
** *
46053 ATCTTCTCTAACCCTAACTGATATTATTCATCATCTTCTTCCTCTGTCTCTG-ATC
1 ATCTTCTCTAACCCTAACACATATTATTCACCATCTTCTTCCTCT-T-T-TGTA-C
*
46108 ATCTTCTATAACCCTA
1 ATCTTCTCTAACCCTA
46124 GATCTAACCA
Statistics
Matches: 61, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
52 40 0.66
53 1 0.02
54 2 0.03
55 18 0.30
ACGTcount: A:0.22, C:0.31, G:0.03, T:0.44
Consensus pattern (52 bp):
ATCTTCTCTAACCCTAACACATATTATTCACCATCTTCTTCCTCTTTTGTAC
Found at i:49542 original size:14 final size:14
Alignment explanation
Indices: 49510--49542 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
49500 TTGAAGATTT
*
49510 ATAACATAAGAATC
1 ATAATATAAGAATC
49524 ATAATATAAGAATC
1 ATAATATAAGAATC
49538 ATAAT
1 ATAAT
49543 TAATATAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.58, C:0.09, G:0.06, T:0.27
Consensus pattern (14 bp):
ATAATATAAGAATC
Found at i:49782 original size:16 final size:16
Alignment explanation
Indices: 49761--49828 Score: 73
Period size: 16 Copynumber: 4.2 Consensus size: 16
49751 TCATTTATAG
*
49761 GTCAGGTTGAAAACAA
1 GTCAGGTTCAAAACAA
*
49777 GTCAGGTTCATAACAA
1 GTCAGGTTCAAAACAA
* * *
49793 GTAAGGTTCATAACAG
1 GTCAGGTTCAAAACAA
* *
49809 GTCAGGTTGAAAACAT
1 GTCAGGTTCAAAACAA
49825 GTCA
1 GTCA
49829 AGCAATACCA
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 44 1.00
ACGTcount: A:0.38, C:0.15, G:0.24, T:0.24
Consensus pattern (16 bp):
GTCAGGTTCAAAACAA
Found at i:52061 original size:132 final size:132
Alignment explanation
Indices: 51824--52100 Score: 527
Period size: 132 Copynumber: 2.1 Consensus size: 132
51814 TGTGTCACTA
*
51824 AATTTTGTAAGTTAAACGTTCAAATTATTTTCATGACAAGATATATCTGGTTTCTTTGTTCGTAA
1 AATTTTGTAAGTTAAACGTTCAAATTATTTTCATGACAAGATATATCTGGTTTATTTGTTCGTAA
*
51889 TGAGATAACATCATCATCAGGGAAGTCTTAGTTGGATCACTCGAGCATAGTAGATGATCAAAACC
66 TGAGATAACATCATCATCAGGGAAGTCTTAGTTGGATCACTCGAGCATAGTAAATGATCAAAACC
51954 TT
131 TT
*
51956 AATTTTGTAAGTTAAATGTTCAAATTATTTTCATGACAAGATATATCTGGTTTATTTGTTCGTAA
1 AATTTTGTAAGTTAAACGTTCAAATTATTTTCATGACAAGATATATCTGGTTTATTTGTTCGTAA
52021 TGAGATAACATCATCATCAGGGAAGTCTTAGTTGGATCACTCGAGCATAGTAAATGATCAAAACC
66 TGAGATAACATCATCATCAGGGAAGTCTTAGTTGGATCACTCGAGCATAGTAAATGATCAAAACC
52086 TT
131 TT
52088 AATTTTGTAAGTT
1 AATTTTGTAAGTT
52101 TATTTGACTG
Statistics
Matches: 142, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
132 142 1.00
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (132 bp):
AATTTTGTAAGTTAAACGTTCAAATTATTTTCATGACAAGATATATCTGGTTTATTTGTTCGTAA
TGAGATAACATCATCATCAGGGAAGTCTTAGTTGGATCACTCGAGCATAGTAAATGATCAAAACC
TT
Found at i:55166 original size:2 final size:2
Alignment explanation
Indices: 55159--55184 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
55149 AACACAATAA
55159 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
55185 TAATAAGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:68736 original size:123 final size:124
Alignment explanation
Indices: 68550--68795 Score: 453
Period size: 124 Copynumber: 2.0 Consensus size: 124
68540 GCATATGAAG
68550 TAGACCCTTGAAAGAATGATCAAATAGAAGAAGATCAAGCTCACCACTCTGGAGCCAAGTG-AAA
1 TAGACCCTTGAAAGAATGATCAAATAGAAGAAGATCAAGCTCACCACTCTGGAGCCAAGTGAAAA
68614 TTGATTCAACATTTATGCATTCATGAGAAACATCATTTGCATAAAAGAAAATGCATTACAC
66 TTGATTCAACATTTATGCATTCATGAG-AACATCA-TTGCATAAAAGAAAATGCATTACAC
68675 TAGACCCTTGAAAG-ATGATCAAATAGAAG-AGATCAAGCTCACCACTCTGGAGCCAAGTGAAAA
1 TAGACCCTTGAAAGAATGATCAAATAGAAGAAGATCAAGCTCACCACTCTGGAGCCAAGTGAAAA
68738 TTGATTCAACATTTATGCATTCATGAGAACATCATTGCATAAAAGAAAATGCATTACA
66 TTGATTCAACATTTATGCATTCATGAGAACATCATTGCATAAAAGAAAATGCATTACA
68796 TGATACATTT
Statistics
Matches: 120, Mismatches: 0, Indels: 5
0.96 0.00 0.04
Matches are distributed among these distances:
122 24 0.20
123 37 0.31
124 45 0.38
125 14 0.12
ACGTcount: A:0.41, C:0.18, G:0.16, T:0.24
Consensus pattern (124 bp):
TAGACCCTTGAAAGAATGATCAAATAGAAGAAGATCAAGCTCACCACTCTGGAGCCAAGTGAAAA
TTGATTCAACATTTATGCATTCATGAGAACATCATTGCATAAAAGAAAATGCATTACAC
Found at i:69610 original size:42 final size:41
Alignment explanation
Indices: 69551--69629 Score: 106
Period size: 41 Copynumber: 1.9 Consensus size: 41
69541 TCATCAGTAA
*
69551 GTCTTTCGAGCATGATGATGAAATCCTTCGGGTCATTTGTAT
1 GTCTTTCGAGCATGATGAT-AAATCCTTCGGGCCATTTGTAT
* *
69593 GTCTTTCGAGTGA-GATGATAAGTCCTTCGGGCCATTT
1 GTCTTTCGAG-CATGATGATAAATCCTTCGGGCCATTT
69630 TAAGCCTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
41 16 0.48
42 16 0.48
43 1 0.03
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (41 bp):
GTCTTTCGAGCATGATGATAAATCCTTCGGGCCATTTGTAT
Found at i:70086 original size:53 final size:53
Alignment explanation
Indices: 70006--70149 Score: 218
Period size: 53 Copynumber: 2.7 Consensus size: 53
69996 GAATCACCAG
70006 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGACAA
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGACAA
* * * *
70059 AAGATTGTTTGAGTTTTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAG
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGACAA
* * *
70112 AAGATTATTCAAATTCTACTCCCTGAA-CAAGAGGGAGC
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGC
70150 AGATCCGTCA
Statistics
Matches: 82, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
52 11 0.13
53 71 0.87
ACGTcount: A:0.32, C:0.21, G:0.26, T:0.22
Consensus pattern (53 bp):
AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGACAA
Found at i:75151 original size:30 final size:30
Alignment explanation
Indices: 75117--75184 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
75107 AATTTCTTAA
*
75117 AATT-AATACTGGAGACTAAATTGAAATTTT
1 AATTAAAT-CTGGAGACTAAAGTGAAATTTT
* * *
75147 AATTAAATTTGGGGACTAAAGTGAATTTTT
1 AATTAAATCTGGAGACTAAAGTGAAATTTT
75177 AATTAAAT
1 AATTAAAT
75185 TCAAATATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 30 0.91
31 3 0.09
ACGTcount: A:0.43, C:0.04, G:0.15, T:0.38
Consensus pattern (30 bp):
AATTAAATCTGGAGACTAAAGTGAAATTTT
Found at i:75728 original size:13 final size:13
Alignment explanation
Indices: 75694--75731 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
75684 AAACGGGTCA
*
75694 ACCCGACCCATCT
1 ACCCGACCCGTCT
*
75707 A-CTGACCCGTCT
1 ACCCGACCCGTCT
75719 ACCCGACCCGTCT
1 ACCCGACCCGTCT
75732 GTCTATCTGA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.18, C:0.50, G:0.13, T:0.18
Consensus pattern (13 bp):
ACCCGACCCGTCT
Found at i:77080 original size:2 final size:2
Alignment explanation
Indices: 77075--77205 Score: 169
Period size: 2 Copynumber: 65.0 Consensus size: 2
77065 ATTTTTTATG
* *
77075 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT -T ACC AT AT GA-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT -AT
* *
77117 AC CT -T ACT GAT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT A-T -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
77160 AT AT AT AT 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 AT AT AT AT
77202 AT AT
1 AT AT
77206 GTTTACCATA
Statistics
Matches: 117, Mismatches: 5, Indels: 14
0.86 0.04 0.10
Matches are distributed among these distances:
1 3 0.03
2 109 0.93
3 4 0.03
4 1 0.01
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:79097 original size:32 final size:32
Alignment explanation
Indices: 79061--79140 Score: 83
Period size: 32 Copynumber: 2.5 Consensus size: 32
79051 ACACATGTTT
* *
79061 AATTATTAATGTGACATGTGACATATCAT-CAA
1 AATTATGAA-GTGACATATGACATATCATCCAA
* *
79093 AATTATGAAGTGTCATATGTCATATCATCCAA
1 AATTATGAAGTGACATATGACATATCATCCAA
*
79125 AATGATGACA-TGACAT
1 AATTATGA-AGTGACAT
79141 GTGTCACCCA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
31 16 0.40
32 23 0.57
33 1 0.03
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.33
Consensus pattern (32 bp):
AATTATGAAGTGACATATGACATATCATCCAA
Found at i:79146 original size:32 final size:32
Alignment explanation
Indices: 79072--79237 Score: 103
Period size: 32 Copynumber: 5.4 Consensus size: 32
79062 ATTATTAATG
* *
79072 TGACATGTGACATATCAT-CAAAATTATGA-A
1 TGACATGTGTCATATCATCCAAAATGATGACA
* *
79102 GTGTCATATGTCATATCATCCAAAATGATGACA
1 -TGACATGTGTCATATCATCCAAAATGATGACA
* *
79135 TGACATGTGTC--A-C--CCAAAATAATGATA
1 TGACATGTGTCATATCATCCAAAATGATGACA
* * * * * * *
79162 TAACATGTATTATGTCATCTAAAGTGATGATA
1 TGACATGTGTCATATCATCCAAAATGATGACA
* ** * *
79194 TGATATGTGTCACGTCATCCAAAGTGATGACG
1 TGACATGTGTCATATCATCCAAAATGATGACA
*
79226 TAACATGTGTCA
1 TGACATGTGTCA
79238 CATAACTAAT
Statistics
Matches: 103, Mismatches: 25, Indels: 13
0.73 0.18 0.09
Matches are distributed among these distances:
27 20 0.19
29 1 0.01
30 2 0.02
31 15 0.15
32 64 0.62
33 1 0.01
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.31
Consensus pattern (32 bp):
TGACATGTGTCATATCATCCAAAATGATGACA
Found at i:87762 original size:22 final size:22
Alignment explanation
Indices: 87715--87763 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 22
87705 AGGTAATTGT
*
87715 TTTTTTATTACTTTTATTCTTG
1 TTTTTTATTACTTTTATTCTTC
87737 TTTTTTATTGA-TTTTGATT-TTC
1 TTTTTTATT-ACTTTT-ATTCTTC
87759 TTTTT
1 TTTTT
87764 CTTTTTAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
22 20 0.83
23 4 0.17
ACGTcount: A:0.12, C:0.06, G:0.06, T:0.76
Consensus pattern (22 bp):
TTTTTTATTACTTTTATTCTTC
Found at i:88091 original size:16 final size:16
Alignment explanation
Indices: 88059--88109 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
88049 TTTAACTTTA
*
88059 TTTTTTAATT-TGA-T
1 TTTTTTGATTCTGACT
88073 TTTTTTGATTCTGACT
1 TTTTTTGATTCTGACT
*
88089 TTTTTCTGTTTCT-ACT
1 TTTTT-TGATTCTGACT
88105 TTTTT
1 TTTTT
88110 CTTAATTTGG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
14 9 0.28
15 3 0.09
16 14 0.44
17 6 0.19
ACGTcount: A:0.12, C:0.10, G:0.08, T:0.71
Consensus pattern (16 bp):
TTTTTTGATTCTGACT
Found at i:88110 original size:16 final size:17
Alignment explanation
Indices: 88072--88111 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
88062 TTTAATTTGA
88072 TTTTTT-TGATTCTGAC
1 TTTTTTCTGATTCTGAC
*
88088 TTTTTTCTGTTTCT-AC
1 TTTTTTCTGATTCTGAC
88104 TTTTTTCT
1 TTTTTTCT
88112 TAATTTGGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 16 0.73
17 6 0.27
ACGTcount: A:0.07, C:0.15, G:0.07, T:0.70
Consensus pattern (17 bp):
TTTTTTCTGATTCTGAC
Found at i:88340 original size:16 final size:17
Alignment explanation
Indices: 88310--88343 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
88300 TTCAATATAA
*
88310 TTTTTTTATTATTTTAT
1 TTTTTTTAGTATTTTAT
88327 TTTTTTTAGT-TTTTAT
1 TTTTTTTAGTATTTTAT
88343 T
1 T
88344 CTTTGAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.15, C:0.00, G:0.03, T:0.82
Consensus pattern (17 bp):
TTTTTTTAGTATTTTAT
Found at i:89585 original size:11 final size:11
Alignment explanation
Indices: 89553--89586 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
89543 ACCAACTGAG
*
89553 CTAAACGAACG
1 CTAAACGAACA
*
89564 CTAAACAAACA
1 CTAAACGAACA
89575 CTAAACGAACA
1 CTAAACGAACA
89586 C
1 C
89587 GTTTGTGGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.53, C:0.29, G:0.09, T:0.09
Consensus pattern (11 bp):
CTAAACGAACA
Found at i:89631 original size:23 final size:23
Alignment explanation
Indices: 89600--89739 Score: 203
Period size: 23 Copynumber: 6.2 Consensus size: 23
89590 TGTGGATATA
* * *
89600 TAAATGAACACGTTTGCGAACAT
1 TAAACGAACATGTTCGCGAACAT
89623 TAAACGAAC--GTTCGCGAACAT
1 TAAACGAACATGTTCGCGAACAT
89644 TAAACGAACATGTTCGCGAACAT
1 TAAACGAACATGTTCGCGAACAT
89667 TAAACGAACATGTTCGCGAACAT
1 TAAACGAACATGTTCGCGAACAT
* *
89690 TAAACGAATATGTTCGTGAACAT
1 TAAACGAACATGTTCGCGAACAT
* *
89713 TAAACGAATATGTTCGCGAACAA
1 TAAACGAACATGTTCGCGAACAT
89736 TAAA
1 TAAA
89740 TAAACAAACA
Statistics
Matches: 109, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
21 20 0.18
23 89 0.82
ACGTcount: A:0.41, C:0.19, G:0.17, T:0.24
Consensus pattern (23 bp):
TAAACGAACATGTTCGCGAACAT
Found at i:89653 original size:11 final size:11
Alignment explanation
Indices: 89616--89697 Score: 58
Period size: 11 Copynumber: 7.4 Consensus size: 11
89606 AACACGTTTG
89616 CGAACATTAAA
1 CGAACATTAAA
* **
89627 CGAACGTT-CG
1 CGAACATTAAA
89637 CGAACATTAAA
1 CGAACATTAAA
***
89648 CGAACATGTTCG
1 CGAACAT-TAAA
89660 CGAACATTAAA
1 CGAACATTAAA
***
89671 CGAACATGTTCG
1 CGAACAT-TAAA
89683 CGAACATTAAA
1 CGAACATTAAA
89694 CGAA
1 CGAA
89698 TATGTTCGTG
Statistics
Matches: 50, Mismatches: 18, Indels: 6
0.68 0.24 0.08
Matches are distributed among these distances:
10 7 0.14
11 27 0.54
12 16 0.32
ACGTcount: A:0.41, C:0.22, G:0.17, T:0.20
Consensus pattern (11 bp):
CGAACATTAAA
Found at i:89665 original size:12 final size:12
Alignment explanation
Indices: 89648--89689 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
89638 GAACATTAAA
89648 CGAACATGTTCG
1 CGAACATGTTCG
***
89660 CGAACAT-TAAA
1 CGAACATGTTCG
89671 CGAACATGTTCG
1 CGAACATGTTCG
89683 CGAACAT
1 CGAACAT
89690 TAAACGAATA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
11 8 0.35
12 15 0.65
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.21
Consensus pattern (12 bp):
CGAACATGTTCG
Found at i:95433 original size:26 final size:26
Alignment explanation
Indices: 95404--95455 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
95394 TCACATATGT
95404 GATATTTATTTAAATTTATATCGGTA
1 GATATTTATTTAAATTTATATCGGTA
95430 GATATTTATTTAAATTTATATCGGTA
1 GATATTTATTTAAATTTATATCGGTA
95456 TAAATTTAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.35, C:0.04, G:0.12, T:0.50
Consensus pattern (26 bp):
GATATTTATTTAAATTTATATCGGTA
Found at i:95462 original size:26 final size:26
Alignment explanation
Indices: 95407--95463 Score: 96
Period size: 26 Copynumber: 2.2 Consensus size: 26
95397 CATATGTGAT
*
95407 ATTTATTTAAATTTATATCGGTAGAT
1 ATTTATTTAAATTTATATCGGTAGAA
*
95433 ATTTATTTAAATTTATATCGGTATAA
1 ATTTATTTAAATTTATATCGGTAGAA
95459 ATTTA
1 ATTTA
95464 AGTATATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.37, C:0.04, G:0.09, T:0.51
Consensus pattern (26 bp):
ATTTATTTAAATTTATATCGGTAGAA
Found at i:95472 original size:26 final size:26
Alignment explanation
Indices: 95414--95472 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 26
95404 GATATTTATT
* **
95414 TAAATTTATATCGGTAGATATTTATT
1 TAAATTTATATCGGTAGAAATTTAAG
*
95440 TAAATTTATATCGGTATAAATTTAAG
1 TAAATTTATATCGGTAGAAATTTAAG
*
95466 TATATTT
1 TAAATTT
95473 TGAGTATAGT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.37, C:0.03, G:0.10, T:0.49
Consensus pattern (26 bp):
TAAATTTATATCGGTAGAAATTTAAG
Found at i:98579 original size:18 final size:19
Alignment explanation
Indices: 98556--98600 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
98546 CACTTGCATA
*
98556 TCAAACTTGCT-AAATTAG
1 TCAAACTTGATAAAATTAG
*
98574 TCAAACTT-ATAAAATTGG
1 TCAAACTTGATAAAATTAG
98592 TCAAACTTG
1 TCAAACTTG
98601 TCAAGCTTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 1 0.04
18 22 0.96
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.33
Consensus pattern (19 bp):
TCAAACTTGATAAAATTAG
Found at i:99854 original size:21 final size:21
Alignment explanation
Indices: 99830--99872 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
99820 CAAAATTGTG
*
99830 CATCGATGCACTGTTACAGTA
1 CATCGATGCACTGCTACAGTA
99851 CATCGATGCACTGCTACAGTA
1 CATCGATGCACTGCTACAGTA
99872 C
1 C
99873 CTTTTGTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.26
Consensus pattern (21 bp):
CATCGATGCACTGCTACAGTA
Found at i:100598 original size:31 final size:31
Alignment explanation
Indices: 100560--100640 Score: 126
Period size: 31 Copynumber: 2.6 Consensus size: 31
100550 TTCATAGATT
* * *
100560 CCGAAGAACCTAGGTAATCAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCAATATGTC
100591 CCGAAGAACATAGGTAAACAGTCAATATGTC
1 CCGAAGAACATAGGTAAACAGTCAATATGTC
*
100622 CCGAAAAACATAGGTAAAC
1 CCGAAGAACATAGGTAAAC
100641 CCTCGACCCT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.41, C:0.22, G:0.19, T:0.19
Consensus pattern (31 bp):
CCGAAGAACATAGGTAAACAGTCAATATGTC
Found at i:104794 original size:3 final size:3
Alignment explanation
Indices: 104786--104814 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
104776 TATTTTTTAC
104786 TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
104815 ATGTAGGTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:111788 original size:20 final size:20
Alignment explanation
Indices: 111765--111808 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
111755 TTTTTTGAAA
*
111765 TTTTGGCTTTTTTT-TTTGTT
1 TTTTGCCTTTTTTTGTTT-TT
111785 TTTTGCCTTTTTTTGTTTTT
1 TTTTGCCTTTTTTTGTTTTT
111805 TTTT
1 TTTT
111809 TAAAATAGCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 19 0.86
21 3 0.14
ACGTcount: A:0.00, C:0.07, G:0.11, T:0.82
Consensus pattern (20 bp):
TTTTGCCTTTTTTTGTTTTT
Found at i:113169 original size:26 final size:26
Alignment explanation
Indices: 113139--113205 Score: 107
Period size: 26 Copynumber: 2.6 Consensus size: 26
113129 GCATGAAATG
*
113139 ATGCATTAAAGGATGGCATAACTAAA
1 ATGCATGAAAGGATGGCATAACTAAA
*
113165 ATGCATGAAAGGATGTCATAACTAAA
1 ATGCATGAAAGGATGGCATAACTAAA
*
113191 ATGCATGAAATGATG
1 ATGCATGAAAGGATG
113206 CATTAAGGCA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.45, C:0.10, G:0.21, T:0.24
Consensus pattern (26 bp):
ATGCATGAAAGGATGGCATAACTAAA
Found at i:113225 original size:20 final size:20
Alignment explanation
Indices: 113193--113384 Score: 150
Period size: 20 Copynumber: 8.7 Consensus size: 20
113183 TAACTAAAAT
*
113193 GCATGAAATGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
* *
113213 GCATAAAAGGATGCCATGACTGAAAT
1 GCATGAAAGGATG-CAT---T--AAG
*
113239 GCATGAAATGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
*
113259 GCATGAAAGGATGCCATAACTAAAAT
1 GCATGAAAGGATG-CAT---T--AAG
113285 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
* * *
113305 ACATGAAAGAATGCCATAACTAAAAT
1 GCATGAAAGGATG-CAT---T--AAG
113331 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
113351 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
113371 GCATGAAAGGATGC
1 GCATGAAAGGATGC
113385 CATAAATGAA
Statistics
Matches: 139, Mismatches: 15, Indels: 36
0.73 0.08 0.19
Matches are distributed among these distances:
20 74 0.53
21 9 0.06
22 3 0.02
24 3 0.02
25 9 0.06
26 41 0.29
ACGTcount: A:0.43, C:0.12, G:0.24, T:0.20
Consensus pattern (20 bp):
GCATGAAAGGATGCATTAAG
Found at i:113239 original size:46 final size:46
Alignment explanation
Indices: 113167--113364 Score: 324
Period size: 46 Copynumber: 4.3 Consensus size: 46
113157 TAACTAAAAT
* *
113167 GCATGAAAGGATGTCATAACTAAAATGCATGAAATGATGCATTAAG
1 GCATGAAAGGATGCCATAACTAAAATGCATGAAAGGATGCATTAAG
* * * *
113213 GCATAAAAGGATGCCATGACTGAAATGCATGAAATGATGCATTAAG
1 GCATGAAAGGATGCCATAACTAAAATGCATGAAAGGATGCATTAAG
113259 GCATGAAAGGATGCCATAACTAAAATGCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCCATAACTAAAATGCATGAAAGGATGCATTAAG
* *
113305 ACATGAAAGAATGCCATAACTAAAATGCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCCATAACTAAAATGCATGAAAGGATGCATTAAG
113351 GCATGAAAGGATGC
1 GCATGAAAGGATGC
113365 ATTAAGGCAT
Statistics
Matches: 140, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 140 1.00
ACGTcount: A:0.43, C:0.13, G:0.23, T:0.21
Consensus pattern (46 bp):
GCATGAAAGGATGCCATAACTAAAATGCATGAAAGGATGCATTAAG
Found at i:113291 original size:26 final size:26
Alignment explanation
Indices: 113259--113344 Score: 112
Period size: 26 Copynumber: 3.5 Consensus size: 26
113249 ATGCATTAAG
113259 GCATGAAAGGATGCCATAACTAAAAT
1 GCATGAAAGGATGCCATAACTAAAAT
*
113285 GCATGAAAGGATG-CAT---TAAGA-
1 GCATGAAAGGATGCCATAACTAAAAT
*
113306 -CATGAAAGAATGCCATAACTAAAAT
1 GCATGAAAGGATGCCATAACTAAAAT
113331 GCATGAAAGGATGC
1 GCATGAAAGGATGC
113345 ATTAAGGCAT
Statistics
Matches: 50, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
20 11 0.22
21 3 0.06
22 4 0.08
24 4 0.08
25 3 0.06
26 25 0.50
ACGTcount: A:0.45, C:0.14, G:0.22, T:0.19
Consensus pattern (26 bp):
GCATGAAAGGATGCCATAACTAAAAT
Found at i:113403 original size:92 final size:89
Alignment explanation
Indices: 113167--113396 Score: 241
Period size: 92 Copynumber: 2.5 Consensus size: 89
113157 TAACTAAAAT
* * * * ** * * *
113167 GCATGAAAGGATGTCATAACTAAAATGCATGAAATGATGCATTAAGGCATAAAAGGATGCCATGA
1 GCATGAAAGGATGCCAT-A-T-AAAGGCATGAAAGGATGCATAAAGAAATGAAAGAATGCCATAA
* *
113232 CTGAAATGCATGAAATGATGCATTAAG
63 CTAAAATGCATGAAAGGATGCATTAAG
* * *
113259 GCATGAAAGGATGCCATAACTAAAATGCATGAAAGGATGCATTAAGACATGAAAGAATGCCATAA
1 GCATGAAAGGATGCCAT-A-T-AAAGGCATGAAAGGATGCATAAAGAAATGAAAGAATGCCATAA
113324 CTAAAATGCATGAAAGGATGCATTAAG
63 CTAAAATGCATGAAAGGATGCATTAAG
113351 GCATGAAAGGATG-CAT-T-AAGGCATGAAAGGATGCCATAAATGAAAT
1 GCATGAAAGGATGCCATATAAAGGCATGAAAGGATG-CATAAA-GAAAT
113397 TAATGAATAA
Statistics
Matches: 125, Mismatches: 11, Indels: 8
0.87 0.08 0.06
Matches are distributed among these distances:
86 15 0.12
87 5 0.04
88 5 0.04
91 3 0.02
92 97 0.78
ACGTcount: A:0.44, C:0.12, G:0.23, T:0.21
Consensus pattern (89 bp):
GCATGAAAGGATGCCATATAAAGGCATGAAAGGATGCATAAAGAAATGAAAGAATGCCATAACTA
AAATGCATGAAAGGATGCATTAAG
Found at i:119586 original size:91 final size:92
Alignment explanation
Indices: 119463--119633 Score: 233
Period size: 91 Copynumber: 1.9 Consensus size: 92
119453 ACAAGGTGAA
* *
119463 GTATCGATACCATGGATCCAGAATATCAAAATGGTATCGATACTTAAA-GA-GTATC-AGTACCA
1 GTATCGATACCATGGATACAGAATATCAAAATGGTATCGATACTGAAAGGAGGTATCGA-TACCA
*
119525 TAGTATAGTAGTATCAATACTGAGAAAG
65 TAGTATAGAAGTATCAATACTGAGAAAG
* *
119553 GTATCGATATCATGCGATATAGAATAT-AGAAATGGTATCGATACTGAAATGGAGGTATCGATAC
1 GTATCGATACCATG-GATACAGAATATCA-AAATGGTATCGATACTGAAA-GGAGGTATCGATAC
119617 CATAGTATAGAAGTATC
63 CATAGTATAGAAGTATC
119634 GGTACTAGGG
Statistics
Matches: 70, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
90 14 0.20
91 29 0.41
93 2 0.03
94 24 0.34
95 1 0.01
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.27
Consensus pattern (92 bp):
GTATCGATACCATGGATACAGAATATCAAAATGGTATCGATACTGAAAGGAGGTATCGATACCAT
AGTATAGAAGTATCAATACTGAGAAAG
Done.