Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004967.1 Hibiscus syriacus cultivar Beakdansim tig00011159_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: 102959
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:887 original size:15 final size:15
Alignment explanation
Indices: 863--918 Score: 69
Period size: 15 Copynumber: 3.7 Consensus size: 15
853 CCCGGAGTTA
863 CGGGTA-CCGGTAAT
1 CGGGTACCCGGTAAT
**
877 CGGGTACCCGGATTTT
1 CGGGTACCCGG-TAAT
893 GCGGGTACCCGGTAAT
1 -CGGGTACCCGGTAAT
909 CGGGTACCCG
1 CGGGTACCCG
919 ATACCTGGTT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
14 6 0.17
15 14 0.40
16 4 0.11
17 11 0.31
ACGTcount: A:0.16, C:0.27, G:0.36, T:0.21
Consensus pattern (15 bp):
CGGGTACCCGGTAAT
Found at i:5067 original size:20 final size:20
Alignment explanation
Indices: 5042--5082 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
5032 AGTTCGCTAA
*
5042 AAAAAAAAAAAAACGAAAAT
1 AAAAAAAAAAAAACAAAAAT
**
5062 AAAAAAATTAAAACAAAAAT
1 AAAAAAAAAAAAACAAAAAT
5082 A
1 A
5083 TAATGAAATG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.83, C:0.05, G:0.02, T:0.10
Consensus pattern (20 bp):
AAAAAAAAAAAAACAAAAAT
Found at i:10640 original size:15 final size:14
Alignment explanation
Indices: 10614--10646 Score: 57
Period size: 15 Copynumber: 2.3 Consensus size: 14
10604 AAAAAGAAAA
10614 ATAATATAATAAAT
1 ATAATATAATAAAT
10628 ATAATAGTAATAAAT
1 ATAATA-TAATAAAT
10643 ATAA
1 ATAA
10647 AAGGGGTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (14 bp):
ATAATATAATAAAT
Found at i:11509 original size:74 final size:72
Alignment explanation
Indices: 11378--11521 Score: 175
Period size: 74 Copynumber: 2.0 Consensus size: 72
11368 TTCTAAATCC
*
11378 TAATTAAAATACTAAAACCATTTAAACTCAAATACAAAGATAAAGATAAAATATAAAAATAATAT
1 TAATTAAAATACTAAAACCATTTAAAC-CAAATACAAAGATAAAAATAAAATAT-AAAATAATAT
11443 CCTAAAAAT
64 CCTAAAAAT
* ** * *
11452 TAATTAAAATACTAAAAAACATATTTAAA-CAAATACAAAGA-AAAAATAATGTTTAAAATATTA
1 TAATTAAAATACT--AAAAC-CATTTAAACCAAATACAAAGATAAAAATAAAATATAAAATAATA
11515 TCCTAAA
63 TCCTAAA
11522 TTTGAGTTTA
Statistics
Matches: 61, Mismatches: 6, Indels: 7
0.82 0.08 0.09
Matches are distributed among these distances:
73 15 0.25
74 22 0.36
75 12 0.20
76 5 0.08
77 7 0.11
ACGTcount: A:0.60, C:0.10, G:0.03, T:0.27
Consensus pattern (72 bp):
TAATTAAAATACTAAAACCATTTAAACCAAATACAAAGATAAAAATAAAATATAAAATAATATCC
TAAAAAT
Found at i:16998 original size:20 final size:20
Alignment explanation
Indices: 16945--17006 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
16935 GATTCCCCTG
16945 TGGGGGGAATCGGTTCCCCTTCA
1 TGGGGGG-ATCGGTT-CCC-TCA
** *
16968 AAGGGGAATCGGTTCCCTCA
1 TGGGGGGATCGGTTCCCTCA
*
16988 TGGGGGGATCGATTCCCTC
1 TGGGGGGATCGGTTCCCTC
17007 TGCACCAAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
20 18 0.56
21 3 0.09
22 7 0.22
23 4 0.12
ACGTcount: A:0.16, C:0.26, G:0.34, T:0.24
Consensus pattern (20 bp):
TGGGGGGATCGGTTCCCTCA
Found at i:23232 original size:17 final size:17
Alignment explanation
Indices: 23210--23245 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
23200 AATGATTAAG
23210 AATCTAAACCATTAAAA
1 AATCTAAACCATTAAAA
*
23227 AATCTAAACTATTAAAA
1 AATCTAAACCATTAAAA
23244 AA
1 AA
23246 ATAAATGATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.61, C:0.14, G:0.00, T:0.25
Consensus pattern (17 bp):
AATCTAAACCATTAAAA
Found at i:23243 original size:16 final size:16
Alignment explanation
Indices: 23204--23244 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 16
23194 GTTATCAATG
*
23204 ATTAAGAATCTAAACC
1 ATTAAAAATCTAAACC
*
23220 ATTAAAAAATCTAAACT
1 ATT-AAAAATCTAAACC
23237 ATTAAAAA
1 ATTAAAAA
23245 AATAAATGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 8 0.36
17 14 0.64
ACGTcount: A:0.59, C:0.12, G:0.02, T:0.27
Consensus pattern (16 bp):
ATTAAAAATCTAAACC
Found at i:23250 original size:16 final size:17
Alignment explanation
Indices: 23214--23259 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
23204 ATTAAGAATC
* *
23214 TAAACCATTAAAAAATC
1 TAAACTATTAAAAAATA
23231 TAAACTATTAAAAAA-A
1 TAAACTATTAAAAAATA
23247 TAAA-TGATTAAAA
1 TAAACT-ATTAAAA
23260 TAGAAAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
15 1 0.04
16 11 0.42
17 14 0.54
ACGTcount: A:0.63, C:0.09, G:0.02, T:0.26
Consensus pattern (17 bp):
TAAACTATTAAAAAATA
Found at i:33335 original size:34 final size:34
Alignment explanation
Indices: 33268--33398 Score: 172
Period size: 34 Copynumber: 3.8 Consensus size: 34
33258 TCATATGTTA
33268 AAGAATGTGATAATATTGCCAAACTTCAAAAGGTG
1 AAGAATGTGATAATA-TGCCAAACTTCAAAAGGTG
* * *
33303 AAGAGTGTGATAATATGTCAAACTTCAGAAGGTG
1 AAGAATGTGATAATATGCCAAACTTCAAAAGGTG
* * * *
33337 AAGAATGTTATTATATGCCCAACTTCAAAAGTTG
1 AAGAATGTGATAATATGCCAAACTTCAAAAGGTG
**
33371 AAGAATGTGATAATATGTTAAACTTCAA
1 AAGAATGTGATAATATGCCAAACTTCAA
33399 GTGTTAAAGG
Statistics
Matches: 81, Mismatches: 15, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
34 67 0.83
35 14 0.17
ACGTcount: A:0.41, C:0.11, G:0.19, T:0.29
Consensus pattern (34 bp):
AAGAATGTGATAATATGCCAAACTTCAAAAGGTG
Found at i:33380 original size:68 final size:69
Alignment explanation
Indices: 33268--33397 Score: 199
Period size: 68 Copynumber: 1.9 Consensus size: 69
33258 TCATATGTTA
*
33268 AAGAATGTGATAATATTGCCAAACTTCAAAAGGTGAAGAGTGTGATAATATGTCAAACTTCAGAA
1 AAGAATGTGATAATATTGCCAAACTTCAAAAGGTGAAGAATGTGATAATATGTCAAACTTCAGAA
33333 GGTG
66 GGTG
* * * * *
33337 AAGAATGTTATTATA-TGCCCAACTTCAAAAGTTGAAGAATGTGATAATATGTTAAACTTCA
1 AAGAATGTGATAATATTGCCAAACTTCAAAAGGTGAAGAATGTGATAATATGTCAAACTTCA
33398 AGTGTTAAAG
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
68 42 0.76
69 13 0.24
ACGTcount: A:0.41, C:0.11, G:0.19, T:0.29
Consensus pattern (69 bp):
AAGAATGTGATAATATTGCCAAACTTCAAAAGGTGAAGAATGTGATAATATGTCAAACTTCAGAA
GGTG
Found at i:38859 original size:13 final size:13
Alignment explanation
Indices: 38841--38866 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
38831 ACATATTTGA
38841 ACAGTCTTCATAT
1 ACAGTCTTCATAT
38854 ACAGTCTTCATAT
1 ACAGTCTTCATAT
38867 GCGCTTCTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (13 bp):
ACAGTCTTCATAT
Found at i:38909 original size:14 final size:14
Alignment explanation
Indices: 38890--38922 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
38880 GGGAAGTAAC
38890 CTCTGC-TAATAAAT
1 CTCTGCATAAT-AAT
38904 CTCTGCATAATAAT
1 CTCTGCATAATAAT
38918 CTCTG
1 CTCTG
38923 TATATAGACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.30, C:0.24, G:0.09, T:0.36
Consensus pattern (14 bp):
CTCTGCATAATAAT
Found at i:39693 original size:42 final size:42
Alignment explanation
Indices: 39640--39735 Score: 156
Period size: 42 Copynumber: 2.3 Consensus size: 42
39630 GCCACGTAAG
39640 ATATAGCGCGGGTCAGAGAACACGCCTGACCTTTATAATTAT
1 ATATAGCGCGGGTCAGAGAACACGCCTGACCTTTATAATTAT
* * **
39682 ATATAGTGCGGGTCAGGGGCCACGCCTGACCTTTATAATTAT
1 ATATAGCGCGGGTCAGAGAACACGCCTGACCTTTATAATTAT
39724 ATATAGCGCGGG
1 ATATAGCGCGGG
39736 GCAGGTACCG
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.26
Consensus pattern (42 bp):
ATATAGCGCGGGTCAGAGAACACGCCTGACCTTTATAATTAT
Found at i:43392 original size:35 final size:34
Alignment explanation
Indices: 43307--43393 Score: 88
Period size: 35 Copynumber: 2.5 Consensus size: 34
43297 AAAATAATTT
* *
43307 TAAATACAACAAACTTACAATAAGTATTAAATGG
1 TAAATACAACAAAATTACAATAAGTATTAAACGG
* *
43341 TAAATGATAACCAAATTACAATAACTGATATTAAACGG
1 TAAAT-ACAACAAAATTACAATAA--G-TATTAAACGG
43379 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
43394 ACTGAAATAC
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.55
36 1 0.02
37 4 0.09
38 10 0.23
ACGTcount: A:0.54, C:0.11, G:0.08, T:0.26
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGTATTAAACGG
Found at i:44467 original size:20 final size:20
Alignment explanation
Indices: 44430--44468 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
44420 GTTATACAAG
*
44430 GGGGGGAATCGGTACCCTCT
1 GGGGGGAATCGATACCCTCT
*
44450 GGGGGGAATCGATTCCCTC
1 GGGGGGAATCGATACCCTC
44469 CGAGCATTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.15, C:0.26, G:0.38, T:0.21
Consensus pattern (20 bp):
GGGGGGAATCGATACCCTCT
Found at i:46782 original size:25 final size:24
Alignment explanation
Indices: 46733--46781 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 24
46723 CAAAACACAA
46733 TAATTTGAAAATTAACATTTTTTT
1 TAATTTGAAAATTAACATTTTTTT
*
46757 TAATTTCGAAAATTTA-ATTTTTTT
1 TAATTT-GAAAATTAACATTTTTTT
46781 T
1 T
46782 TGAAAATTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 15 0.65
25 8 0.35
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.57
Consensus pattern (24 bp):
TAATTTGAAAATTAACATTTTTTT
Found at i:46990 original size:20 final size:20
Alignment explanation
Indices: 46953--46991 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
46943 AGATTGAGTG
* * *
46953 GATTTTGATGTTGTTTGCAC
1 GATTTTAATGATGATTGCAC
46973 GATTTTAATGATGATTGCA
1 GATTTTAATGATGATTGCA
46992 AGTTTAGGAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.23, C:0.08, G:0.23, T:0.46
Consensus pattern (20 bp):
GATTTTAATGATGATTGCAC
Found at i:47219 original size:20 final size:20
Alignment explanation
Indices: 47190--47227 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
47180 CCCCTTCAAA
*
47190 GGGGGAATCGGTTCCCTCAT
1 GGGGGAATCGATTCCCTCAT
*
47210 GGGGGGATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
47228 TGCACCAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.26, G:0.37, T:0.24
Consensus pattern (20 bp):
GGGGGAATCGATTCCCTCAT
Found at i:49418 original size:18 final size:19
Alignment explanation
Indices: 49363--49426 Score: 82
Period size: 17 Copynumber: 3.5 Consensus size: 19
49353 CGAAACCGGT
49363 TTTTTCGGTTCGGTTCGGG
1 TTTTTCGGTTCGGTTCGGG
*
49382 TTTTT---TAACGGTTCGGG
1 TTTTTCGGT-TCGGTTCGGG
49399 TTTTTCGGTTCGGTTC-GG
1 TTTTTCGGTTCGGTTCGGG
49417 TTTTTCGGTT
1 TTTTTCGGTT
49427 TTTCAATGAA
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
16 1 0.03
17 14 0.36
18 12 0.31
19 11 0.28
20 1 0.03
ACGTcount: A:0.03, C:0.14, G:0.31, T:0.52
Consensus pattern (19 bp):
TTTTTCGGTTCGGTTCGGG
Found at i:59636 original size:22 final size:22
Alignment explanation
Indices: 59594--59640 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
59584 TATAGCAGGG
* *
59594 TATTGTTCACGATATTGTTCAT
1 TATTGTTCACGATACTATTCAT
59616 TATTGTTCAC-AGTACTATTCAT
1 TATTGTTCACGA-TACTATTCAT
59638 TAT
1 TAT
59641 GTATTTTACT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 21 0.95
ACGTcount: A:0.26, C:0.15, G:0.11, T:0.49
Consensus pattern (22 bp):
TATTGTTCACGATACTATTCAT
Found at i:65504 original size:2 final size:2
Alignment explanation
Indices: 65497--65523 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
65487 CAATAAAGAC
65497 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
65524 GTAGAACGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:77816 original size:20 final size:20
Alignment explanation
Indices: 77791--77835 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
77781 ACATTGCTCT
77791 TGTTCTTTCTAACAAAGTTA
1 TGTTCTTTCTAACAAAGTTA
77811 TGTTCTTTCTAACAAAGTTA
1 TGTTCTTTCTAACAAAGTTA
77831 TGTTC
1 TGTTC
77836 ATCCGCTCTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.27, C:0.16, G:0.11, T:0.47
Consensus pattern (20 bp):
TGTTCTTTCTAACAAAGTTA
Found at i:82427 original size:15 final size:16
Alignment explanation
Indices: 82396--82430 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
82386 TTTGATTTAG
*
82396 ATCAAATCGAGTTCGA
1 ATCAAATCGAATTCGA
82412 ATCAAATC-AATTCGA
1 ATCAAATCGAATTCGA
82427 ATCA
1 ATCA
82431 TTTTCAGATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.43, C:0.20, G:0.11, T:0.26
Consensus pattern (16 bp):
ATCAAATCGAATTCGA
Found at i:84675 original size:12 final size:12
Alignment explanation
Indices: 84660--84713 Score: 72
Period size: 12 Copynumber: 4.5 Consensus size: 12
84650 GAACAACTTC
*
84660 AGGAAGTTGAGG
1 AGGAAGTTGAAG
84672 AGGAAGTTGAAG
1 AGGAAGTTGAAG
* *
84684 AAGAAGTAGAAG
1 AGGAAGTTGAAG
*
84696 AGGAGGTTGAAG
1 AGGAAGTTGAAG
84708 AGGAAG
1 AGGAAG
84714 AGGAAGTGGA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 35 1.00
ACGTcount: A:0.43, C:0.00, G:0.44, T:0.13
Consensus pattern (12 bp):
AGGAAGTTGAAG
Found at i:84719 original size:24 final size:24
Alignment explanation
Indices: 84671--84759 Score: 72
Period size: 24 Copynumber: 3.7 Consensus size: 24
84661 GGAAGTTGAG
* *
84671 GAGGAAGTTGAAGAAGAAGTA-GAA
1 GAGGAGGTTGAAGAGGAAG-AGGAA
84695 GAGGAGGTTGAAGAGGAAGAGGAA
1 GAGGAGGTTGAAGAGGAAGAGGAA
* * * * * *
84719 GTGGAGCTGGATGAGGACGAGGAC
1 GAGGAGGTTGAAGAGGAAGAGGAA
**
84743 GAGGAGGAAGAAGAGGA
1 GAGGAGGTTGAAGAGGA
84760 CGAAGAGGAC
Statistics
Matches: 51, Mismatches: 13, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
23 1 0.02
24 50 0.98
ACGTcount: A:0.40, C:0.03, G:0.47, T:0.09
Consensus pattern (24 bp):
GAGGAGGTTGAAGAGGAAGAGGAA
Found at i:89250 original size:2 final size:2
Alignment explanation
Indices: 89243--89271 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
89233 AAGAACTTTC
89243 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
89272 CTATGTTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:93240 original size:62 final size:62
Alignment explanation
Indices: 93143--93268 Score: 198
Period size: 62 Copynumber: 2.0 Consensus size: 62
93133 GTGGAATTGA
*
93143 TTTTGTAACCTTCACACATTTAGCTATAAATTCTCAGATGCGAACCTTGTACGGTCAATTAC
1 TTTTGTAACCTTCACACATTTAGCTATAAATTCTCAGATGCGAACCTTATACGGTCAATTAC
** * * *
93205 TTTTGTAAGGTTCATACATTTGGCTATAAATTCTCAGATGTGAACCTTATACGGTCAATTAC
1 TTTTGTAACCTTCACACATTTAGCTATAAATTCTCAGATGCGAACCTTATACGGTCAATTAC
93267 TT
1 TT
93269 GTGATATCTA
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
62 58 1.00
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (62 bp):
TTTTGTAACCTTCACACATTTAGCTATAAATTCTCAGATGCGAACCTTATACGGTCAATTAC
Found at i:95801 original size:20 final size:20
Alignment explanation
Indices: 95771--95966 Score: 189
Period size: 20 Copynumber: 9.7 Consensus size: 20
95761 GTTTCCAGAT
*
95771 TCGCAACGCGATTCTGACTA
1 TCGCAATGCGATTCTGACTA
* * *
95791 TCGCATTGCGATTTTG-CAAA
1 TCGCAATGCGATTCTGAC-TA
** *
95811 TTCGCGTTGCGATTTTCCGACTA
1 -TCGCAATGCGA--TTCTGACTA
* * *
95834 TCGCAATGCGAATATGTA-AA
1 TCGCAATGCGATTCTG-ACTA
*
95854 TCGCAATGCGATTATGACTA
1 TCGCAATGCGATTCTGACTA
*
95874 TCGCAGTGCGATTCTGACTA
1 TCGCAATGCGATTCTGACTA
* *
95894 TCGCAACGAGATTCTGACTA
1 TCGCAATGCGATTCTGACTA
*
95914 TCGCAACGCGATTCTGACTA
1 TCGCAATGCGATTCTGACTA
*
95934 TCGCAACGCGATTCTGACTA
1 TCGCAATGCGATTCTGACTA
95954 TCGCAATGCGATT
1 TCGCAATGCGATT
95967 TTCAAAGCGC
Statistics
Matches: 146, Mismatches: 23, Indels: 14
0.80 0.13 0.08
Matches are distributed among these distances:
19 2 0.01
20 119 0.82
21 11 0.08
22 9 0.06
23 4 0.03
24 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (20 bp):
TCGCAATGCGATTCTGACTA
Found at i:96181 original size:22 final size:22
Alignment explanation
Indices: 96130--96182 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
96120 CACTCTCTAA
* *
96130 GGCGACATCCGTCCCCATCTCC
1 GGCGAAATCAGTCCCCATCTCC
* *
96152 GACAAAATCAGTCCCCATCTCC
1 GGCGAAATCAGTCCCCATCTCC
96174 GGCGAAATC
1 GGCGAAATC
96183 CATCTATCTC
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.25, C:0.42, G:0.17, T:0.17
Consensus pattern (22 bp):
GGCGAAATCAGTCCCCATCTCC
Found at i:96526 original size:20 final size:20
Alignment explanation
Indices: 96503--96543 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
96493 CATTCGATAG
96503 TCATTTTCGTATTGCGATTT
1 TCATTTTCGTATTGCGATTT
*
96523 TCATTTTCGTGTTGCGATTT
1 TCATTTTCGTATTGCGATTT
96543 T
1 T
96544 AAGTTTCAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.12, C:0.15, G:0.17, T:0.56
Consensus pattern (20 bp):
TCATTTTCGTATTGCGATTT
Found at i:96550 original size:20 final size:20
Alignment explanation
Indices: 96507--96550 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
96497 CGATAGTCAT
* *
96507 TTTCGTATTGCGATTTTCAT
1 TTTCGTATTGCGATTTTAAG
*
96527 TTTCGTGTTGCGATTTTAAG
1 TTTCGTATTGCGATTTTAAG
96547 TTTC
1 TTTC
96551 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.14, C:0.14, G:0.18, T:0.55
Consensus pattern (20 bp):
TTTCGTATTGCGATTTTAAG
Found at i:98294 original size:18 final size:18
Alignment explanation
Indices: 98271--98320 Score: 100
Period size: 18 Copynumber: 2.8 Consensus size: 18
98261 TTTACTCGTA
98271 ATTTCACTTAGATTAACC
1 ATTTCACTTAGATTAACC
98289 ATTTCACTTAGATTAACC
1 ATTTCACTTAGATTAACC
98307 ATTTCACTTAGATT
1 ATTTCACTTAGATT
98321 GCTTAGTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.32, C:0.20, G:0.06, T:0.42
Consensus pattern (18 bp):
ATTTCACTTAGATTAACC
Found at i:98497 original size:20 final size:20
Alignment explanation
Indices: 98472--98515 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
98462 TTACTTTCGT
98472 AACGCGAAAATGACTATCGC
1 AACGCGAAAATGACTATCGC
**
98492 AACGCGAATTTGACTATCGC
1 AACGCGAAAATGACTATCGC
98512 AACG
1 AACG
98516 AAAAAATCGC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.18
Consensus pattern (20 bp):
AACGCGAAAATGACTATCGC
Found at i:98605 original size:20 final size:20
Alignment explanation
Indices: 98580--98625 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
98570 ACATTCGCGT
98580 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
**
98600 TCGCAACGCGAATTTGACTA
1 TCGCAACGCGAAAATGACTA
98620 TCGCAA
1 TCGCAA
98626 AAAAAATCGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.20
Consensus pattern (20 bp):
TCGCAACGCGAAAATGACTA
Found at i:99283 original size:24 final size:23
Alignment explanation
Indices: 99218--99284 Score: 57
Period size: 21 Copynumber: 3.0 Consensus size: 23
99208 GCCTCCCTTT
*
99218 CGTTCAAGAGGCCTCTATCATCC
1 CGTTCAAGAGGCCACTATCATCC
** * *
99241 C--TCAAGAATCCCCTCTCATCAC
1 CGTTCAAGAGGCCACTATCATC-C
*
99263 CGTTCAAGAGGCCACTGTCATC
1 CGTTCAAGAGGCCACTATCATC
99285 GTTGAAGAGG
Statistics
Matches: 33, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
21 15 0.45
22 2 0.06
23 1 0.03
24 15 0.45
ACGTcount: A:0.24, C:0.37, G:0.15, T:0.24
Consensus pattern (23 bp):
CGTTCAAGAGGCCACTATCATCC
Found at i:100662 original size:13 final size:14
Alignment explanation
Indices: 100628--100665 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
100618 TTGCTTGTTT
*
100628 AATTGATTTATAAA
1 AATTGATTTGTAAA
100642 AATTGATTTGT-AA
1 AATTGATTTGTAAA
*
100655 AGTTGATTTGT
1 AATTGATTTGT
100666 TTAATATTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 12 0.55
14 10 0.45
ACGTcount: A:0.37, C:0.00, G:0.16, T:0.47
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:100818 original size:14 final size:14
Alignment explanation
Indices: 100799--100828 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
100789 ACGCTAAACC
*
100799 AAATCGCAATGCGA
1 AAATCGCAACGCGA
100813 AAATCGCAACGCGA
1 AAATCGCAACGCGA
100827 AA
1 AA
100829 GTCAATTCGC
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:0.47, C:0.23, G:0.20, T:0.10
Consensus pattern (14 bp):
AAATCGCAACGCGA
Found at i:100882 original size:34 final size:34
Alignment explanation
Indices: 100838--100964 Score: 128
Period size: 34 Copynumber: 3.6 Consensus size: 34
100828 AGTCAATTCG
* * *
100838 CGTTGTGATAGTCTAATACGCTTTGCGATTTTCT
1 CGTTGCGATAGTCAAATACGCGTTGCGATTTTCT
* *
100872 CGTTGCGATAGTCAAATACCCGTTGCGATAATCAAGTTCG
1 CGTTGCGATAGTCAAATACGCGTTGCGAT--T----TTCT
* *
100912 CGTTGCGATAGTCAAATTCGCGTTGCGTTTTTCT
1 CGTTGCGATAGTCAAATACGCGTTGCGATTTTCT
*
100946 CGTTACGATAGTCAAATAC
1 CGTTGCGATAGTCAAATAC
100965 CCATTGCAAT
Statistics
Matches: 76, Mismatches: 11, Indels: 12
0.77 0.11 0.12
Matches are distributed among these distances:
34 45 0.59
36 1 0.01
38 1 0.01
40 29 0.38
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.35
Consensus pattern (34 bp):
CGTTGCGATAGTCAAATACGCGTTGCGATTTTCT
Found at i:100897 original size:20 final size:20
Alignment explanation
Indices: 100872--101109 Score: 136
Period size: 20 Copynumber: 12.8 Consensus size: 20
100862 GCGATTTTCT
* *
100872 CGTTGCGATAGTCAAATACC
1 CGTTGCGATAGTCAAATTCG
* *
100892 CGTTGCGATAATCAAGTTCG
1 CGTTGCGATAGTCAAATTCG
100912 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* *
100932 CGTTGCG-T--T---TTTCT
1 CGTTGCGATAGTCAAATTCG
* * *
100946 CGTTACGATAGTCAAATACC
1 CGTTGCGATAGTCAAATTCG
* * *
100966 CATTGCAATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* *
100986 CGTTGC-A-A-T---TTTTG
1 CGTTGCGATAGTCAAATTCG
*
101000 TGTTGCGATAGTC--ATTCG
1 CGTTGCGATAGTCAAATTCG
*
101018 TGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* *
101038 CGTTGCGAT--T---TTTTG
1 CGTTGCGATAGTCAAATTCG
* *
101053 AGTTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* *
101073 CGTTGCAATAGTCAAATTTG
1 CGTTGCGATAGTCAAATTCG
*
101093 CGTTGCGATATTCAAAT
1 CGTTGCGATAGTCAAAT
101110 GAATGTGTAA
Statistics
Matches: 165, Mismatches: 36, Indels: 34
0.70 0.15 0.14
Matches are distributed among these distances:
14 17 0.10
15 13 0.08
16 1 0.01
17 5 0.03
18 18 0.11
19 2 0.01
20 109 0.66
ACGTcount: A:0.25, C:0.18, G:0.21, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:100955 original size:74 final size:73
Alignment explanation
Indices: 100830--100991 Score: 234
Period size: 74 Copynumber: 2.2 Consensus size: 73
100820 AACGCGAAAG
* * * * *
100830 TCAATTCGCGTTGTGATAGTCTAATACGCTTTGCGATTTTCTCGTTGCGATAGTCAAATACCCGT
1 TCAATTCGCGTTGCGATAGTCAAATACGCGTTGCGATTTTCTCGTTACGATAGTCAAATACCCAT
*
100895 TGCGATAA
66 TGCAATAA
* *
100903 TCAAGTTCGCGTTGCGATAGTCAAATTCGCGTTGCGTTTTTCTCGTTACGATAGTCAAATACCCA
1 TCAA-TTCGCGTTGCGATAGTCAAATACGCGTTGCGATTTTCTCGTTACGATAGTCAAATACCCA
100968 TTGCAATAA
65 TTGCAATAA
100977 TCAAATTCGCGTTGC
1 TC-AATTCGCGTTGC
100992 AATTTTTGTG
Statistics
Matches: 79, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
73 4 0.05
74 73 0.92
75 2 0.03
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.35
Consensus pattern (73 bp):
TCAATTCGCGTTGCGATAGTCAAATACGCGTTGCGATTTTCTCGTTACGATAGTCAAATACCCAT
TGCAATAA
Found at i:100987 original size:54 final size:52
Alignment explanation
Indices: 100893--101099 Score: 220
Period size: 54 Copynumber: 3.9 Consensus size: 52
100883 TCAAATACCC
* * *
100893 GTTGCGATAATCAAGTTCGCGTTGCGATAGTCAAATTCGCGTTGCGTTTTTCT
1 GTTGCGATAGTCAAATTCGCGTTGCAATAGTCAAATTCGCGTTGCGTTTTT-T
* * * * * *
100946 CGTTACGATAGTCAAATACCCATTGCAATAATCAAATTCGCGTTGCAATTTTTGT
1 -GTTGCGATAGTCAAATTCGCGTTGCAATAGTCAAATTCGCGTTGC-GTTTTT-T
* *
101001 GTTGCGATAGTC--ATTCGTGTTGCGATAGTCAAATTCGCGTTGCGATTTTTT
1 GTTGCGATAGTCAAATTCGCGTTGCAATAGTCAAATTCGCGTTGCG-TTTTTT
* *
101052 GAGTTGCGATAATCAAATTCGCGTTGCAATAGTCAAATTTGCGTTGCG
1 --GTTGCGATAGTCAAATTCGCGTTGCAATAGTCAAATTCGCGTTGCG
101100 ATATTCAAAT
Statistics
Matches: 125, Mismatches: 22, Indels: 11
0.79 0.14 0.07
Matches are distributed among these distances:
51 1 0.01
52 30 0.24
53 11 0.09
54 48 0.38
55 35 0.28
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.36
Consensus pattern (52 bp):
GTTGCGATAGTCAAATTCGCGTTGCAATAGTCAAATTCGCGTTGCGTTTTTT
Found at i:101022 original size:18 final size:19
Alignment explanation
Indices: 100999--101046 Score: 71
Period size: 18 Copynumber: 2.5 Consensus size: 19
100989 TGCAATTTTT
100999 GTGTTGCGATAGTC-ATTC
1 GTGTTGCGATAGTCAATTC
101017 GTGTTGCGATAGTCAAATTC
1 GTGTTGCGATAGTC-AATTC
*
101037 GCGTTGCGAT
1 GTGTTGCGAT
101047 TTTTTGAGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 14 0.52
20 13 0.48
ACGTcount: A:0.19, C:0.17, G:0.29, T:0.35
Consensus pattern (19 bp):
GTGTTGCGATAGTCAATTC
Found at i:101158 original size:70 final size:70
Alignment explanation
Indices: 101084--101298 Score: 169
Period size: 70 Copynumber: 3.1 Consensus size: 70
101074 GTTGCAATAG
*
101084 TCAAATTTGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCATAGC
1 TCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCATAGC
101149 AATGT
66 AATGT
* ** * * * * * *
101154 TCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGT-TAA-AAGT--TTAC-ACAT-AAAAT
1 TCAAATTCGCGTTGC-GAT--AT-TC-AAATG--AATGTGTAATAAGTGATAACAAC-TGAACAT
* *
101213 A-CACA-TAATAG-
58 ATCATAGCAAT-GT
*
101224 TCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCATAGC
1 TCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCATAGC
101289 AATGT
66 AATGT
101294 TCAAA
1 TCAAA
101299 CTCAAGTTAC
Statistics
Matches: 103, Mismatches: 24, Indels: 36
0.63 0.15 0.22
Matches are distributed among these distances:
63 5 0.05
64 3 0.03
65 8 0.08
66 1 0.01
67 6 0.06
68 6 0.06
69 6 0.06
70 32 0.31
71 6 0.06
72 7 0.07
73 6 0.06
74 1 0.01
75 8 0.08
76 3 0.03
77 5 0.05
ACGTcount: A:0.42, C:0.15, G:0.14, T:0.29
Consensus pattern (70 bp):
TCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCATAGC
AATGT
Found at i:101331 original size:140 final size:140
Alignment explanation
Indices: 101079--101349 Score: 515
Period size: 140 Copynumber: 1.9 Consensus size: 140
101069 TTCGCGTTGC
* *
101079 AATAGTCAAATTTGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATC
1 AATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATC
101144 ATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATA
66 ATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATA
101209 AAATACACAT
131 AAATACACAT
101219 AATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATC
1 AATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATC
*
101284 ATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACATATA
66 ATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATA
101349 A
131 A
101350 TACAACGTTT
Statistics
Matches: 128, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
140 128 1.00
ACGTcount: A:0.42, C:0.15, G:0.14, T:0.29
Consensus pattern (140 bp):
AATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATC
ATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATA
AAATACACAT
Found at i:101430 original size:18 final size:18
Alignment explanation
Indices: 101404--101444 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
101394 AGGTGAAGCC
*
101404 GATTGTGATTGGGATTTT
1 GATTGTGATTGCGATTTT
*
101422 GATTTTGATTGCGATTTT
1 GATTGTGATTGCGATTTT
101440 GATTG
1 GATTG
101445 CCTTTTTCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.17, C:0.02, G:0.29, T:0.51
Consensus pattern (18 bp):
GATTGTGATTGCGATTTT
Found at i:101497 original size:18 final size:19
Alignment explanation
Indices: 101474--101524 Score: 77
Period size: 19 Copynumber: 2.7 Consensus size: 19
101464 TGAGCTTTGG
101474 ATTTTGAT-GAGGATCCAT
1 ATTTTGATAGAGGATCCAT
*
101492 ATTTTGGTAGAGGATCCAT
1 ATTTTGATAGAGGATCCAT
*
101511 ATTTTGGTAGAGGA
1 ATTTTGATAGAGGA
101525 AAAGATGATT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
18 7 0.23
19 24 0.77
ACGTcount: A:0.27, C:0.08, G:0.27, T:0.37
Consensus pattern (19 bp):
ATTTTGATAGAGGATCCAT
Found at i:101506 original size:19 final size:19
Alignment explanation
Indices: 101482--101524 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
101472 GGATTTTGAT
101482 GAGGATCCATATTTTGGTA
1 GAGGATCCATATTTTGGTA
101501 GAGGATCCATATTTTGGTA
1 GAGGATCCATATTTTGGTA
101520 GAGGA
1 GAGGA
101525 AAAGATGATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.28, C:0.09, G:0.30, T:0.33
Consensus pattern (19 bp):
GAGGATCCATATTTTGGTA
Done.