Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003863.1 Hibiscus syriacus cultivar Beakdansim tig00008310_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: 112299
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:3280 original size:21 final size:21
Alignment explanation
Indices: 3243--3328 Score: 77
Period size: 21 Copynumber: 4.0 Consensus size: 21
3233 TTTTGGTGCA
*
3243 GAGGGAATCGA-TCCCCCCCT
1 GAGGGAACCGATTCCCCCCCT
**
3263 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCCT
*
3284 GAATGGGAACCGATTCCCCCCACA
1 G-A-GGGAACCGATTCCCCCC-CT
* *
3308 G-GGGAATCGATACCCCCCCT
1 GAGGGAACCGATTCCCCCCCT
3328 G
1 G
3329 GGGTTCTGTT
Statistics
Matches: 53, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
20 12 0.23
21 23 0.43
22 1 0.02
23 16 0.30
24 1 0.02
ACGTcount: A:0.22, C:0.37, G:0.24, T:0.16
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCCT
Found at i:8050 original size:21 final size:21
Alignment explanation
Indices: 8006--8081 Score: 136
Period size: 21 Copynumber: 3.7 Consensus size: 21
7996 TTGCAGCCTT
*
8006 GATGCATGGATGCATGGC-AG
1 GATGCATCGATGCATGGCAAG
8026 GATGCATCGATGCATGGCAAG
1 GATGCATCGATGCATGGCAAG
8047 GATGCATCGATGCATGGCAAG
1 GATGCATCGATGCATGGCAAG
8068 GATGCATCGATGCA
1 GATGCATCGATGCA
8082 CTAATTGCAT
Statistics
Matches: 54, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
20 17 0.31
21 37 0.69
ACGTcount: A:0.28, C:0.18, G:0.34, T:0.20
Consensus pattern (21 bp):
GATGCATCGATGCATGGCAAG
Found at i:8170 original size:21 final size:21
Alignment explanation
Indices: 8144--8201 Score: 116
Period size: 21 Copynumber: 2.8 Consensus size: 21
8134 CATTAGTGCA
8144 GATGCATGGATGCACTGCAGG
1 GATGCATGGATGCACTGCAGG
8165 GATGCATGGATGCACTGCAGG
1 GATGCATGGATGCACTGCAGG
8186 GATGCATGGATGCACT
1 GATGCATGGATGCACT
8202 TTGACACCCT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.24, C:0.19, G:0.36, T:0.21
Consensus pattern (21 bp):
GATGCATGGATGCACTGCAGG
Found at i:8340 original size:30 final size:30
Alignment explanation
Indices: 8283--8342 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
8273 AACTTTGAAT
8283 AAATTCAATTCAAATCCAAAAACATTTTGC
1 AAATTCAATTCAAATCCAAAAACATTTTGC
*
8313 AAATTCAATTCAAGTCCAAAAACATTTTGC
1 AAATTCAATTCAAATCCAAAAACATTTTGC
8343 CTTAAATTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.45, C:0.20, G:0.05, T:0.30
Consensus pattern (30 bp):
AAATTCAATTCAAATCCAAAAACATTTTGC
Found at i:9027 original size:11 final size:11
Alignment explanation
Indices: 9011--9042 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
9001 ATATTTGACT
9011 ATTTCTGAATA
1 ATTTCTGAATA
9022 ATTTCTGAATA
1 ATTTCTGAATA
9033 ATTTCTGAAT
1 ATTTCTGAAT
9043 CATGGATTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.34, C:0.09, G:0.09, T:0.47
Consensus pattern (11 bp):
ATTTCTGAATA
Found at i:13813 original size:27 final size:27
Alignment explanation
Indices: 13782--13854 Score: 112
Period size: 27 Copynumber: 2.7 Consensus size: 27
13772 TATGAAATTT
*
13782 TTTGTCTCGAAGGACCTA-TGTACTGTA
1 TTTGTCTCGAATGACC-ACTGTACTGTA
*
13809 TTTGTCCCGAATGACCACTGTACTGTA
1 TTTGTCTCGAATGACCACTGTACTGTA
13836 TTTGTCTCGAATGACCACT
1 TTTGTCTCGAATGACCACT
13855 CCTTAAGAAC
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
26 1 0.02
27 41 0.98
ACGTcount: A:0.22, C:0.23, G:0.19, T:0.36
Consensus pattern (27 bp):
TTTGTCTCGAATGACCACTGTACTGTA
Found at i:15665 original size:29 final size:29
Alignment explanation
Indices: 15630--15711 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
15620 AAACTAAATT
*
15630 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
15659 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
15688 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
15712 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:20434 original size:29 final size:29
Alignment explanation
Indices: 20399--20480 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
20389 AAACTAAATT
*
20399 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
20428 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
20457 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
20481 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:24124 original size:56 final size:55
Alignment explanation
Indices: 24037--24147 Score: 159
Period size: 56 Copynumber: 2.0 Consensus size: 55
24027 CGACTTCGAC
* * *
24037 AAATCCCATCTAATAGGGCAATCATTATTGGCTAGACCGAAAACAAAACAGATAGT
1 AAATCACATCAAATAGGGCAACCATTATTGGCTAG-CCGAAAACAAAACAGATAGT
* **
24093 AAATCACATCAAATAGGGCAACCATTCTTGGCTAGCCGAAAACAGCACAGATAGT
1 AAATCACATCAAATAGGGCAACCATTATTGGCTAGCCGAAAACAAAACAGATAGT
24148 GTCCACCTTA
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
55 18 0.37
56 31 0.63
ACGTcount: A:0.41, C:0.22, G:0.17, T:0.20
Consensus pattern (55 bp):
AAATCACATCAAATAGGGCAACCATTATTGGCTAGCCGAAAACAAAACAGATAGT
Found at i:26275 original size:31 final size:32
Alignment explanation
Indices: 26224--26284 Score: 97
Period size: 31 Copynumber: 1.9 Consensus size: 32
26214 CAACAAATTT
**
26224 CCTAAAAGTATATTTAAAAAATATATATTTTC
1 CCTAAAAACATATTTAAAAAATATATATTTTC
26256 CCTAAAAACATATTT-AAAAATATATATTT
1 CCTAAAAACATATTTAAAAAATATATATTT
26285 AAAAAAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 14 0.52
32 13 0.48
ACGTcount: A:0.49, C:0.10, G:0.02, T:0.39
Consensus pattern (32 bp):
CCTAAAAACATATTTAAAAAATATATATTTTC
Found at i:26533 original size:13 final size:14
Alignment explanation
Indices: 26512--26546 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
26502 TTTCATTAGG
*
26512 TTAATATTTATT-A
1 TTAAGATTTATTAA
26525 TTAAGATTTATTAA
1 TTAAGATTTATTAA
26539 TTAAGATT
1 TTAAGATT
26547 ATATATATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 11 0.55
14 9 0.45
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (14 bp):
TTAAGATTTATTAA
Found at i:30291 original size:15 final size:15
Alignment explanation
Indices: 30266--30300 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
30256 GGTTTGTTGA
30266 AAATA-AAATAAAAT
1 AAATATAAATAAAAT
*
30280 AGATATAAATAAAAT
1 AAATATAAATAAAAT
30295 AAATAT
1 AAATAT
30301 CATCTTTTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
14 4 0.22
15 14 0.78
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (15 bp):
AAATATAAATAAAAT
Found at i:30921 original size:26 final size:26
Alignment explanation
Indices: 30883--30955 Score: 137
Period size: 26 Copynumber: 2.8 Consensus size: 26
30873 CCTTATTTTA
*
30883 TATTAATAATACATTTCAATACATAT
1 TATTAATAGTACATTTCAATACATAT
30909 TATTAATAGTACATTTCAATACATAT
1 TATTAATAGTACATTTCAATACATAT
30935 TATTAATAGTACATTTCAATA
1 TATTAATAGTACATTTCAATA
30956 AATGGTCCTA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 46 1.00
ACGTcount: A:0.44, C:0.11, G:0.03, T:0.42
Consensus pattern (26 bp):
TATTAATAGTACATTTCAATACATAT
Found at i:39229 original size:16 final size:16
Alignment explanation
Indices: 39205--39236 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
39195 AATAAGCCAG
*
39205 CTGTTTGTCCTTATAA
1 CTGTCTGTCCTTATAA
39221 CTGTCTGTCCTTATAA
1 CTGTCTGTCCTTATAA
39237 TAACCTATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.22, G:0.12, T:0.47
Consensus pattern (16 bp):
CTGTCTGTCCTTATAA
Found at i:42121 original size:19 final size:19
Alignment explanation
Indices: 42097--42136 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
42087 ATTTGGTTTC
42097 TTTTTAAAAATATATAATT
1 TTTTTAAAAATATATAATT
42116 TTTTTAAAAATATATAATT
1 TTTTTAAAAATATATAATT
42135 TT
1 TT
42137 ATTTTTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TTTTTAAAAATATATAATT
Found at i:49466 original size:16 final size:16
Alignment explanation
Indices: 49442--49473 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
49432 AATAAGCCAG
*
49442 CTGTTTGTCCTTATAA
1 CTGTCTGTCCTTATAA
49458 CTGTCTGTCCTTATAA
1 CTGTCTGTCCTTATAA
49474 TAACCTATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.22, G:0.12, T:0.47
Consensus pattern (16 bp):
CTGTCTGTCCTTATAA
Found at i:54022 original size:2 final size:2
Alignment explanation
Indices: 54015--54044 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
54005 ATATCAATAC
54015 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
54045 GCATGTATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:59057 original size:24 final size:23
Alignment explanation
Indices: 58983--59062 Score: 78
Period size: 24 Copynumber: 3.5 Consensus size: 23
58973 CATAACCCCG
58983 TGCATCGATGCACATTCAAGGCG-
1 TGCATCGATGCACATTCAAGG-GA
* *
59006 TGCATCGGTGCATCA-TC-A-TGA
1 TGCATCGATGCA-CATTCAAGGGA
*
59027 TGAATCGATGCACATTCAAAGGGA
1 TGCATCGATGCACATTC-AAGGGA
59051 TGCATCGATGCA
1 TGCATCGATGCA
59063 TGAAGCACAT
Statistics
Matches: 45, Mismatches: 6, Indels: 11
0.73 0.10 0.18
Matches are distributed among these distances:
20 3 0.07
21 12 0.27
22 1 0.02
23 14 0.31
24 15 0.33
ACGTcount: A:0.29, C:0.23, G:0.25, T:0.24
Consensus pattern (23 bp):
TGCATCGATGCACATTCAAGGGA
Found at i:62457 original size:13 final size:13
Alignment explanation
Indices: 62439--62466 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
62429 CTCCTTTTCC
62439 TACAAACATAGAT
1 TACAAACATAGAT
62452 TACAAACATAGAT
1 TACAAACATAGAT
62465 TA
1 TA
62467 ATTTCTAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.54, C:0.14, G:0.07, T:0.25
Consensus pattern (13 bp):
TACAAACATAGAT
Found at i:65007 original size:65 final size:65
Alignment explanation
Indices: 64851--65034 Score: 191
Period size: 65 Copynumber: 2.8 Consensus size: 65
64841 ACCATTGGAC
* * *
64851 CCTTAGTGCATCGGTGCACT-A-AGAGTGCATCTATCCATCAAGT-TCATTCGATG-TTTCAAAA
1 CCTTAGTGCATCGGTGCA-TGATA-AGTGCATCGATGCATCAAATGT-ATTCGATGTTTTCAAAA
64912 TAG
63 TAG
** *
64915 CCAGAGTGCATCGATGCATGACT-AGTGCATCGATGCATCAAATGTATTCGATGTTTTCATAAA-
1 CCTTAGTGCATCGGTGCATGA-TAAGTGCATCGATGCATCAAATGTATTCGATGTTTTCA-AAAT
*
64978 AT
64 AG
* * *
64980 CCTTAGTGCATCGGTGCATGATAAGTGCTTCGATGCATGAAATGCATTCGATGTT
1 CCTTAGTGCATCGGTGCATGATAAGTGCATCGATGCATCAAATGTATTCGATGTT
65035 CAATTTAATT
Statistics
Matches: 100, Mismatches: 13, Indels: 13
0.79 0.10 0.10
Matches are distributed among these distances:
63 1 0.01
64 42 0.42
65 54 0.54
66 3 0.03
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.32
Consensus pattern (65 bp):
CCTTAGTGCATCGGTGCATGATAAGTGCATCGATGCATCAAATGTATTCGATGTTTTCAAAATAG
Found at i:65031 original size:18 final size:19
Alignment explanation
Indices: 64984--65032 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
64974 TAAAATCCTT
* *
64984 AGTGCATCGGTGCATGATA
1 AGTGCTTCGATGCATGATA
65003 AGTGCTTCGATGCATGA-A
1 AGTGCTTCGATGCATGATA
65021 A-TGCATTCGATG
1 AGTGC-TTCGATG
65033 TTCAATTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 3 0.11
18 9 0.33
19 15 0.56
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.29
Consensus pattern (19 bp):
AGTGCTTCGATGCATGATA
Found at i:65082 original size:65 final size:64
Alignment explanation
Indices: 64874--65084 Score: 201
Period size: 65 Copynumber: 3.3 Consensus size: 64
64864 GTGCACTAAG
* * * * * * *
64874 AGTGCATCTATCCATCAAGTTCATTCGATGTTTCA-AAATAGCCAGAGTGCATCGATGCATGACT
1 AGTGCATCGATGCATCAAATGCATTCGATGTTTCATAAA-ATCCATAGTGCATCGATGCATGATT
* * * *
64938 AGTGCATCGATGCATCAAATGTATTCGATGTTTTCATAAAATCCTTAGTGCATCGGTGCATGATA
1 AGTGCATCGATGCATCAAATGCATTCGATG-TTTCATAAAATCCATAGTGCATCGATGCATGATT
* * ** * *
65003 AGTGCTTCGATGCATGAAATGCATTCGATG-TTCAATTTAATTCATGGTGCATCGATGCATGGAT
1 AGTGCATCGATGCATCAAATGCATTCGATGTTTC-ATAAAATCCATAGTGCATCGATGCAT-GAT
65067 T
64 T
* *
65068 GGTGCATCGGTGCATCA
1 AGTGCATCGATGCATCA
65085 CTCTGAAAAA
Statistics
Matches: 118, Mismatches: 25, Indels: 7
0.79 0.17 0.05
Matches are distributed among these distances:
63 3 0.03
64 45 0.38
65 67 0.57
66 3 0.03
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.32
Consensus pattern (64 bp):
AGTGCATCGATGCATCAAATGCATTCGATGTTTCATAAAATCCATAGTGCATCGATGCATGATT
Found at i:67833 original size:30 final size:28
Alignment explanation
Indices: 67791--67872 Score: 74
Period size: 29 Copynumber: 2.8 Consensus size: 28
67781 ATTAATTACT
* *
67791 AAAGAATGGAGCCATAATTGTAATGATCA
1 AAAGAATGGAGCC-TAATTATAAAGATCA
* *
67820 AAAGAGTGAGAGCCTAATTATAAAGATTA
1 AAAGAATG-GAGCCTAATTATAAAGATCA
* * *
67849 AAAGTATAGAGCCCTAAGTATAAA
1 AAAGAATGGAG-CCTAATTATAAA
67873 TATTAAAGGA
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
28 3 0.07
29 35 0.81
30 5 0.12
ACGTcount: A:0.48, C:0.10, G:0.20, T:0.23
Consensus pattern (28 bp):
AAAGAATGGAGCCTAATTATAAAGATCA
Found at i:68965 original size:18 final size:18
Alignment explanation
Indices: 68942--68976 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
68932 ATATTTGATA
68942 ATTAAAAAAATTAATTAT
1 ATTAAAAAAATTAATTAT
* *
68960 ATTAAAAGAATTTATTA
1 ATTAAAAAAATTAATTA
68977 AATAAATTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (18 bp):
ATTAAAAAAATTAATTAT
Found at i:69398 original size:16 final size:17
Alignment explanation
Indices: 69360--69400 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
69350 GAGTATTTAA
* *
69360 AATTATTTTATATTTTT
1 AATTATTTAATATTATT
69377 AA-TATTTAATA-TATT
1 AATTATTTAATATTATT
69392 AATTATTTA
1 AATTATTTA
69401 TAATGTTATG
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 5 0.24
16 14 0.67
17 2 0.10
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
AATTATTTAATATTATT
Found at i:70507 original size:21 final size:21
Alignment explanation
Indices: 70470--70531 Score: 108
Period size: 21 Copynumber: 3.0 Consensus size: 21
70460 CCGTTAGACA
70470 GGGGGAATCGGTA-CCCCTGG
1 GGGGGAATCGGTACCCCCTGG
70490 GGGGGAATCGGTACCCCCTGG
1 GGGGGAATCGGTACCCCCTGG
*
70511 GGGGGAATCGATACCCCCTGG
1 GGGGGAATCGGTACCCCCTGG
70532 ACAATCTGAT
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
20 13 0.32
21 27 0.68
ACGTcount: A:0.16, C:0.27, G:0.42, T:0.15
Consensus pattern (21 bp):
GGGGGAATCGGTACCCCCTGG
Found at i:72025 original size:19 final size:20
Alignment explanation
Indices: 71982--72029 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
71972 TCTAAATCCT
*
71982 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
72002 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
72021 TTTTCAAAA
1 TTTTCAAAA
72030 GAAAATCATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:73353 original size:21 final size:20
Alignment explanation
Indices: 73306--73406 Score: 114
Period size: 21 Copynumber: 4.9 Consensus size: 20
73296 CCATTAGACA
73306 GGGGGAATCGGTACCCC-TG
1 GGGGGAATCGGTACCCCTTG
* *
73325 GGGGGAATCTGTTCCCCTTG
1 GGGGGAATCGGTACCCCTTG
*
73345 GGGGTGAATCGGTACCCCCTGG
1 GGGG-GAATCGGTA-CCCCTTG
*
73367 GGGGGAATCGGTACCCCCTTCA
1 GGGGGAATCGGTA-CCCCTT-G
*
73389 GGGGGAATCTGTACCCCT
1 GGGGGAATCGGTACCCCT
73407 AGACAATCTG
Statistics
Matches: 70, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
19 15 0.21
20 6 0.09
21 27 0.39
22 22 0.31
ACGTcount: A:0.15, C:0.28, G:0.37, T:0.21
Consensus pattern (20 bp):
GGGGGAATCGGTACCCCTTG
Found at i:73965 original size:20 final size:20
Alignment explanation
Indices: 73936--73975 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
73926 TGTAAAAATT
* *
73936 AAATTTAAAAAATATATTCA
1 AAATTAAAAAAAAATATTCA
73956 AAATTAAAAAAAAATATTCA
1 AAATTAAAAAAAAATATTCA
73976 CTAATTTTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (20 bp):
AAATTAAAAAAAAATATTCA
Found at i:74735 original size:15 final size:15
Alignment explanation
Indices: 74717--74772 Score: 67
Period size: 15 Copynumber: 3.6 Consensus size: 15
74707 TAACCGGTTT
74717 CGGTTTTAAAAAAAC
1 CGGTTTTAAAAAAAC
*
74732 CGGTTTTTTTAAAAAAC
1 CGG--TTTTAAAAAAAC
*
74749 CGGTTATAAAAAAAC
1 CGGTTTTAAAAAAAC
*
74764 CGATTTTAA
1 CGGTTTTAA
74773 TATTCCAGAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
15 20 0.59
17 14 0.41
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.32
Consensus pattern (15 bp):
CGGTTTTAAAAAAAC
Found at i:74745 original size:17 final size:17
Alignment explanation
Indices: 74720--74770 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
74710 CCGGTTTCGG
74720 TTTTAAAAAAACCGGTT
1 TTTTAAAAAAACCGGTT
*
74737 TTTTTAAAAAACCGG--
1 TTTTAAAAAAACCGGTT
* *
74752 TTATAAAAAAACCGATT
1 TTTTAAAAAAACCGGTT
74769 TT
1 TT
74771 AATATTCCAG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 12 0.43
17 16 0.57
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.35
Consensus pattern (17 bp):
TTTTAAAAAAACCGGTT
Found at i:75189 original size:13 final size:13
Alignment explanation
Indices: 75168--75222 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
75158 AAGTTCGATA
*
75168 AATTCAAATACTT
1 AATTGAAATACTT
75181 AATTGAAATACTT
1 AATTGAAATACTT
* *
75194 AATT-AACTCAACAT
1 AATTGAAAT--ACTT
75208 AATTGAAATACTT
1 AATTGAAATACTT
75221 AA
1 AA
75223 ATACTTCCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.35
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:75304 original size:32 final size:33
Alignment explanation
Indices: 75208--75306 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
75198 AACTCAACAT
* * *
75208 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
75241 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
75274 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
75306 A
1 A
75307 TTGAAACAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 12 0.19
33 51 0.81
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.32
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:75325 original size:21 final size:21
Alignment explanation
Indices: 75301--75340 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
75291 ACTTCAAGTT
75301 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
75322 CGATAATTGAAATAAAGTT
1 CGATAATTGAAACAAAGTT
75341 ATAAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.30
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:77649 original size:12 final size:12
Alignment explanation
Indices: 77632--77674 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 12
77622 GGATAAAAAT
77632 CGGTTTTTTAAC
1 CGGTTTTTTAAC
77644 CGGTTTTTTTCAAAC
1 CGG-TTTTTT--AAC
*
77659 CGGTTTTTTATC
1 CGGTTTTTTAAC
77671 CGGT
1 CGGT
77675 AAAAAAACCG
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
12 9 0.33
13 6 0.22
14 6 0.22
15 6 0.22
ACGTcount: A:0.14, C:0.19, G:0.19, T:0.49
Consensus pattern (12 bp):
CGGTTTTTTAAC
Found at i:79956 original size:18 final size:19
Alignment explanation
Indices: 79933--79972 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
79923 TTCGTAATAA
79933 TTTTATT-CACTGATAATC
1 TTTTATTACACTGATAATC
79951 TTTTATTCACACTGATAATC
1 TTTTATT-ACACTGATAATC
79971 TT
1 TT
79973 ATATCCCATC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 7 0.35
20 13 0.65
ACGTcount: A:0.28, C:0.17, G:0.05, T:0.50
Consensus pattern (19 bp):
TTTTATTACACTGATAATC
Found at i:80162 original size:2 final size:2
Alignment explanation
Indices: 80155--80200 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
80145 TTCAACTTCC
80155 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
80197 CT CT
1 CT CT
80201 GTATATATAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:91271 original size:37 final size:37
Alignment explanation
Indices: 91198--91272 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 37
91188 GTTGGAAAAT
* *
91198 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
* *
91235 ATTTATATAATTTTTTTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTAAAAAATTGAAAATCATAAA
91272 A
1 A
91273 AGGTTTAATG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 14 0.42
38 19 0.58
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
Found at i:92504 original size:34 final size:33
Alignment explanation
Indices: 92448--92513 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 33
92438 GGTTGCAAAG
** *
92448 ATATAAATTTATATATATTTTTTTGAATTTTTTT
1 ATATAAATTTATATA-AAATTTTTAAATTTTTTT
92482 ATATAAATTTAT-TGAAAATTTTTAAATTTTTT
1 ATATAAATTTATAT-AAAATTTTTAAATTTTTT
92514 CTCACATGAC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
33 15 0.54
34 13 0.46
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (33 bp):
ATATAAATTTATATAAAATTTTTAAATTTTTTT
Found at i:95122 original size:22 final size:22
Alignment explanation
Indices: 95097--95145 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
95087 ACTTTTTGGG
95097 TGAAATGAATTAACTA-TTTTCA
1 TGAAAT-AATTAACTATTTTTCA
*
95119 TGAAAATACTTAACTATTTTTCA
1 TG-AAATAATTAACTATTTTTCA
95142 TGAA
1 TGAA
95146 TGTAGATGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
22 12 0.50
23 12 0.50
ACGTcount: A:0.41, C:0.10, G:0.08, T:0.41
Consensus pattern (22 bp):
TGAAATAATTAACTATTTTTCA
Found at i:95125 original size:23 final size:23
Alignment explanation
Indices: 95099--95145 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
95089 TTTTTGGGTG
95099 AAATGAATTAACTA-TTTTCATGA
1 AAAT-AATTAACTATTTTTCATGA
*
95122 AAATACTTAACTATTTTTCATGA
1 AAATAATTAACTATTTTTCATGA
95145 A
1 A
95146 TGTAGATGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 8 0.36
23 14 0.64
ACGTcount: A:0.43, C:0.11, G:0.06, T:0.40
Consensus pattern (23 bp):
AAATAATTAACTATTTTTCATGA
Found at i:99001 original size:324 final size:324
Alignment explanation
Indices: 98412--99371 Score: 1609
Period size: 324 Copynumber: 3.0 Consensus size: 324
98402 AGCCTGATCG
* * * *
98412 AATTGAGGTTAATCAAGCATTAGAACTTCAAAATAAGATCAGTGTACTGAAGAAAGAAAATCAAC
1 AATTGAGGTTAATCAAGCGTTAGAACTTCAAAATAAGATCAGCGTACTGGAGAAAGAAAAGCAAC
* * ** *
98477 ATGTTGATAGCAAGATGCAGGCATTGTTGGAAGAGTTAAGTGTTACTAAAGAAATGCTTGAGGGT
66 ATGTTGATAGCAAGCTGCAGGCATTGTTGGAAGAATTAAGCATTACTAAAGAAATGCTCGAGGGT
* * *
98542 TCCGAGAAAGAAAATGCTAGTCTGAAGCTTGA-GAAGAAGCAGTTTTATGAGAAAATTCAAAATT
131 TCCGAGAAAGAAAATGCTAGTTTGAAGCTTCACG-AGAAGCAGTTTTATGAGAAAATTCAAGATT
98606 TGCAGTGTCAGCTCGATACGGCTCAAAGAGAAATTGTGGAGTTGAAACTGGAGCTTGCTGAGAGA
195 TGCAGTGTCAGCTCGATACGGCTCAAAGAGAAATTGTGGAGTTGAAACTGGAGCTTGCTGAGAGA
* * * *
98671 AGCAGCTGCATGGAAATCTTGAATGAAGACCTTGAGACTTTGAAATTTGAGTGCAGGAGGCTTAA
260 AGCAGCTGCATGGAAATCTTGAATGAAGACCTTGAGACTTCGAAATTGGAGAGCAGAAGGCTTAA
98736 AATTGAGGTTAATCAAGCGTTAGAACTTCAAAATAAGATCAGCGTACTGGAGAAAGAAAAGCAAC
1 AATTGAGGTTAATCAAGCGTTAGAACTTCAAAATAAGATCAGCGTACTGGAGAAAGAAAAGCAAC
98801 ATGTTGATAGCAAGCTGCAGGCATTGTTGGAAGAATTAAGCATTACTAAAGAAATGCTCGAGGGT
66 ATGTTGATAGCAAGCTGCAGGCATTGTTGGAAGAATTAAGCATTACTAAAGAAATGCTCGAGGGT
*
98866 TCCGAGAAAGAAAATGCTAGTTTGAAGCTTCACGAGAAGCAGTTTTATGATAAAATTCAAGATTT
131 TCCGAGAAAGAAAATGCTAGTTTGAAGCTTCACGAGAAGCAGTTTTATGAGAAAATTCAAGATTT
*
98931 GCAGTGTCAGCTCGATACGGCTCAAAGAGAAATTGTGGAGTTGAAACTGGAGCTTGCTGAGAAAA
196 GCAGTGTCAGCTCGATACGGCTCAAAGAGAAATTGTGGAGTTGAAACTGGAGCTTGCTGAGAGAA
*
98996 GCAGCTGCATGGAAATCTTGAATGAAGACCTTGAGACTTCGAGATTGGAGAGCAGAAGGCTTAA
261 GCAGCTGCATGGAAATCTTGAATGAAGACCTTGAGACTTCGAAATTGGAGAGCAGAAGGCTTAA
*
99060 AATTGAGGTTAATCAAGCGTTAGAACTTCAAAATAAGATCGGCGTACTGGAGAAAGAAAAGCAAC
1 AATTGAGGTTAATCAAGCGTTAGAACTTCAAAATAAGATCAGCGTACTGGAGAAAGAAAAGCAAC
*
99125 ATGTTGACAGCAAGCTGCAGGCATTGTTGGAAGAATTAAGCATTACTAAAGAAATGCTCGAGGGT
66 ATGTTGATAGCAAGCTGCAGGCATTGTTGGAAGAATTAAGCATTACTAAAGAAATGCTCGAGGGT
99190 TCCGAGAAAGAAAATGCTAGTTTGAAGCTTCACGAGAAGCAGTTTTATGAGAAAATTCAAGATTT
131 TCCGAGAAAGAAAATGCTAGTTTGAAGCTTCACGAGAAGCAGTTTTATGAGAAAATTCAAGATTT
* * * *
99255 GCAGTGTCAGCTCGATACGGTTCAAAGAGAAATTGCGGAGTTGAAACTGGAGCTTGTTGAGAGCA
196 GCAGTGTCAGCTCGATACGGCTCAAAGAGAAATTGTGGAGTTGAAACTGGAGCTTGCTGAGAGAA
* * * * * *
99320 GCAGTTGTAT-TAAAGTCTTAAATGAAGACCTTGAGACTTCAAAATCGGAGAG
261 GCAGCTGCATGGAAA-TCTTGAATGAAGACCTTGAGACTTCGAAATTGGAGAG
99372 AAACGTGCTT
Statistics
Matches: 600, Mismatches: 34, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
323 3 0.00
324 596 0.99
325 1 0.00
ACGTcount: A:0.36, C:0.13, G:0.26, T:0.24
Consensus pattern (324 bp):
AATTGAGGTTAATCAAGCGTTAGAACTTCAAAATAAGATCAGCGTACTGGAGAAAGAAAAGCAAC
ATGTTGATAGCAAGCTGCAGGCATTGTTGGAAGAATTAAGCATTACTAAAGAAATGCTCGAGGGT
TCCGAGAAAGAAAATGCTAGTTTGAAGCTTCACGAGAAGCAGTTTTATGAGAAAATTCAAGATTT
GCAGTGTCAGCTCGATACGGCTCAAAGAGAAATTGTGGAGTTGAAACTGGAGCTTGCTGAGAGAA
GCAGCTGCATGGAAATCTTGAATGAAGACCTTGAGACTTCGAAATTGGAGAGCAGAAGGCTTAA
Found at i:99932 original size:17 final size:17
Alignment explanation
Indices: 99910--99944 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
99900 GATCTGATGC
*
99910 ATAATGCAAGTATTCTT
1 ATAATGCAAGTAATCTT
99927 ATAATGCAAGTAATCTT
1 ATAATGCAAGTAATCTT
99944 A
1 A
99945 CCAATAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.37
Consensus pattern (17 bp):
ATAATGCAAGTAATCTT
Found at i:105765 original size:60 final size:62
Alignment explanation
Indices: 105664--105788 Score: 191
Period size: 61 Copynumber: 2.0 Consensus size: 62
105654 ATAATTTTTA
* * *
105664 TTTTTAAGTTAATATATTTTAAAAATATATATGTTCGTATTATATTCGTA-TAATAATAAAT
1 TTTTTAAGTTAATATATTTTAAAAATATATATATTCGTATTATATTCATATTAAAAATAAAT
* *
105725 TTTTTAAGTTAATATATTTTAAAAA-ATATATATTCTTATTATATTCATATTAAAAATATAT
1 TTTTTAAGTTAATATATTTTAAAAATATATATATTCGTATTATATTCATATTAAAAATAAAT
105786 TTT
1 TTT
105789 ATATAATTTA
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
60 21 0.36
61 37 0.64
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.51
Consensus pattern (62 bp):
TTTTTAAGTTAATATATTTTAAAAATATATATATTCGTATTATATTCATATTAAAAATAAAT
Found at i:105789 original size:137 final size:137
Alignment explanation
Indices: 105577--105842 Score: 437
Period size: 137 Copynumber: 1.9 Consensus size: 137
105567 ACATATTAAA
*
105577 ATAATAATAAAATATTTTAAGTCAATATATTTTAAAAATATATATCCTATTATATTCGTATTAAA
1 ATAATAATAAAATATTTTAAGTCAATATATTTTAAAAATATATATCCTATTATATTCATATTAAA
* *
105642 AATATATTTTATATAATTTTTATTTTTAAGTTAATATATTTTAAAA-ATATATATGTTCGTATTA
66 AATATATTTTATATAATTTATATTTTTAAGTTAATATATTTTAAAATATATATATATTCGTATTA
105706 TATTCGT
131 TATTCGT
* * *
105713 ATAATAAT-AAATTTTTTAAGTTAATATATTTTAAAAAATATATATTCTTATTATATTCATATTA
1 ATAATAATAAAATATTTTAAGTCAATATATTTT-AAAAATATATA-TCCTATTATATTCATATTA
*
105777 AAAATATATTTTATATAATTTATATTTTTAAGTTAATATATTTTAAAATATATATATATTTGTAT
64 AAAATATATTTTATATAATTTATATTTTTAAGTTAATATATTTTAAAATATATATATATTCGTAT
105842 T
129 T
105843 TTTTTGTTAA
Statistics
Matches: 120, Mismatches: 7, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
135 22 0.18
136 19 0.16
137 64 0.53
138 15 0.12
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (137 bp):
ATAATAATAAAATATTTTAAGTCAATATATTTTAAAAATATATATCCTATTATATTCATATTAAA
AATATATTTTATATAATTTATATTTTTAAGTTAATATATTTTAAAATATATATATATTCGTATTA
TATTCGT
Found at i:105801 original size:60 final size:60
Alignment explanation
Indices: 105664--105807 Score: 175
Period size: 61 Copynumber: 2.4 Consensus size: 60
105654 ATAATTTTTA
* * *
105664 TTTTTAAGTTAATATATTTTAAAAATATATATGTTCGTATTATATTCGTATAATAATAAAT
1 TTTTTAAGTT-ATATATTTTAAAAATATATATATTCGTATTATATTCATATAAAAATAAAT
* *
105725 TTTTTAAGTTAATATATTTTAAAAA-ATATATATTCTTATTATATTCATATTAAAAATATAT
1 TTTTTAAGTT-ATATATTTTAAAAATATATATATTCGTATTATATTCATA-TAAAAATAAAT
*
105786 TTTATATAATTTATAT-TTTTAA
1 TTT-T-TAAGTTATATATTTTAA
105808 GTTAATATAT
Statistics
Matches: 74, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
60 21 0.28
61 43 0.58
62 5 0.07
63 5 0.07
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (60 bp):
TTTTTAAGTTATATATTTTAAAAATATATATATTCGTATTATATTCATATAAAAATAAAT
Found at i:111864 original size:15 final size:15
Alignment explanation
Indices: 111820--111866 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
111810 GCTGTCATCA
*
111820 TCATCGTCATCGTCA
1 TCATCGTCATCGTCG
* *
111835 CCATTGTCATCGTCG
1 TCATCGTCATCGTCG
111850 TCATCGTCATCGTCG
1 TCATCGTCATCGTCG
111865 TC
1 TC
111867 GTCCTGAGCA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.15, C:0.34, G:0.17, T:0.34
Consensus pattern (15 bp):
TCATCGTCATCGTCG
Done.