Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002438.1 Hibiscus syriacus cultivar Beakdansim tig00004992_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: 112600
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:19623 original size:23 final size:22
Alignment explanation
Indices: 19597--19640 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
19587 GTTTAATATA
19597 AATTA-AATAAAAATATATGTTTG
1 AATTATAA-AAAAAT-TATGTTTG
19620 AATTATTAAAAAAATTATGTT
1 AATTA-TAAAAAAATTATGTT
19641 GGTCTAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
24 6 0.32
25 2 0.11
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (22 bp):
AATTATAAAAAAATTATGTTTG
Found at i:19902 original size:29 final size:30
Alignment explanation
Indices: 19859--19916 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
19849 TCCACTTTTT
19859 TAGTTTAGTGCCTAACG-TTTATTTCGTTC
1 TAGTTTAGTGCCTAACGTTTTATTTCGTTC
* * *
19888 TAGTTTGGTGTCTAATGTTTTATTTCGTT
1 TAGTTTAGTGCCTAACGTTTTATTTCGTT
19917 ACTCAAAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 14 0.56
30 11 0.44
ACGTcount: A:0.16, C:0.12, G:0.19, T:0.53
Consensus pattern (30 bp):
TAGTTTAGTGCCTAACGTTTTATTTCGTTC
Found at i:20056 original size:24 final size:24
Alignment explanation
Indices: 20010--20057 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
20000 TTATATAAAA
* *
20010 TTAAAAAAGAAAATTATATATTTT
1 TTAAAAAAGAAAATCATAAATTTT
20034 TTAAAAAAGAAACA-CATAAATTTT
1 TTAAAAAAGAAA-ATCATAAATTTT
20058 GAAATAACCC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 20 0.95
25 1 0.05
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.35
Consensus pattern (24 bp):
TTAAAAAAGAAAATCATAAATTTT
Found at i:20609 original size:30 final size:28
Alignment explanation
Indices: 20570--20640 Score: 72
Period size: 29 Copynumber: 2.5 Consensus size: 28
20560 CATTTTAAAT
* *
20570 AACAGAATAAAACATTATACACTAAACTGA
1 AACAAAAT-AAACATTAGACACTAAACT-A
* *
20600 AACAAAATAAACGTTAGACATTAAACTA
1 AACAAAATAAACATTAGACACTAAACTA
*
20628 AA-AAAATTAACAT
1 AACAAAATAAACAT
20641 AGATTAAACA
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
27 9 0.26
28 3 0.09
29 16 0.46
30 7 0.20
ACGTcount: A:0.59, C:0.14, G:0.06, T:0.21
Consensus pattern (28 bp):
AACAAAATAAACATTAGACACTAAACTA
Found at i:27330 original size:35 final size:35
Alignment explanation
Indices: 27283--27368 Score: 100
Period size: 35 Copynumber: 2.5 Consensus size: 35
27273 AAAACAATCA
* * *
27283 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
* * * *
27318 TCAATTTTATTCTAAACCCTAAATTCTAAAATACT
1 TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
*
27353 TCAATTAAATTCTAAA
1 TCAATTTAATTCTAAA
27369 ATACTTCAAT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.41, C:0.21, G:0.01, T:0.37
Consensus pattern (35 bp):
TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
Found at i:27362 original size:21 final size:21
Alignment explanation
Indices: 27337--27379 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
27327 TTCTAAACCC
27337 TAAATTCTAAAATACTTCAAT
1 TAAATTCTAAAATACTTCAAT
27358 TAAATTCTAAAATACTTCAAT
1 TAAATTCTAAAATACTTCAAT
27379 T
1 T
27380 TAAGGTAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATTCTAAAATACTTCAAT
Found at i:27531 original size:16 final size:18
Alignment explanation
Indices: 27499--27532 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
27489 TATTAATGTA
27499 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
27517 TGAAT-ATTT-TATTTTT
1 TGAATCATTTATATTTTT
27533 AATAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:28198 original size:130 final size:130
Alignment explanation
Indices: 27995--28242 Score: 424
Period size: 130 Copynumber: 1.9 Consensus size: 130
27985 AATTTTCTTC
* *
27995 TAATTAGGAGGTGACATGTGTCACCAATAACACATATCATGATCATGTGTTAACACATGTCAGAT
1 TAATTAGGAGGTAACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
* *
28060 CCTGATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 CCTAATTAAATGATTAATTTATTAAATGTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* * * *
28125 TAATTAGGTGGTAACATGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGAGGTAACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
28190 CCTAATTAAATGATTAATTTATTAAATGTTATTTAATTTAGGACCAAATTGAT
66 CCTAATTAAATGATTAATTTATTAAATGTTATTTAATTTAGGACCAAATTGAT
28243 TATATAAATA
Statistics
Matches: 110, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
130 110 1.00
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (130 bp):
TAATTAGGAGGTAACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
CCTAATTAAATGATTAATTTATTAAATGTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:47445 original size:36 final size:35
Alignment explanation
Indices: 47404--47522 Score: 141
Period size: 36 Copynumber: 3.3 Consensus size: 35
47394 CTCCTACTTT
* *
47404 TGCTTCTATGAAAGGATCTTAAAGGACTTCTGCTGA
1 TGCTTCTCTGAAA-GATCTTACAGGACTTCTGCTGA
* *
47440 TGCTTCGCCTCAAAGATCTTACAGGACTTCTGCTGA
1 TGCTTC-TCTGAAAGATCTTACAGGACTTCTGCTGA
*
47476 TGGTTCTCCTCG-AAGATCTTACAGGACTTCTGCTGA
1 TGCTTCT-CT-GAAAGATCTTACAGGACTTCTGCTGA
*
47512 CGCTTCTCTGA
1 TGCTTCTCTGA
47523 GAGCGTGCTC
Statistics
Matches: 70, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
34 1 0.01
35 2 0.03
36 63 0.90
37 4 0.06
ACGTcount: A:0.22, C:0.24, G:0.21, T:0.33
Consensus pattern (35 bp):
TGCTTCTCTGAAAGATCTTACAGGACTTCTGCTGA
Found at i:49214 original size:24 final size:21
Alignment explanation
Indices: 49165--49215 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
49155 CAGAATCACT
*
49165 ATCAGAATCTGATGATTCTGA
1 ATCAGAATCTGAAGATTCTGA
*
49186 CTCAGAATCTGAAGAACTCTCTGA
1 ATCAGAATCTGAAG-A-T-TCTGA
49210 ATCAGA
1 ATCAGA
49216 TGAATAATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 12 0.50
22 1 0.04
23 1 0.04
24 10 0.42
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (21 bp):
ATCAGAATCTGAAGATTCTGA
Found at i:56486 original size:44 final size:43
Alignment explanation
Indices: 56426--56536 Score: 143
Period size: 43 Copynumber: 2.6 Consensus size: 43
56416 ACAATTTAGG
* * *
56426 AGTCTCAATTACAAAAGTAAAAAATGGGATTAAAAAAAATTAAG
1 AGTCTCAATTATAAAAGTAAAAAATGAGATT-AAAAAAATTAAA
* * *
56470 AG-CTTTAATTATAAAAGTAAAAAGTGATATTAAAAAAATTAAA
1 AGTC-TCAATTATAAAAGTAAAAAATGAGATTAAAAAAATTAAA
56513 AGTCTCAATTATAAAAGTAAAAAA
1 AGTCTCAATTATAAAAGTAAAAAA
56537 ATACGATTGA
Statistics
Matches: 57, Mismatches: 8, Indels: 5
0.81 0.11 0.07
Matches are distributed among these distances:
43 32 0.56
44 25 0.44
ACGTcount: A:0.58, C:0.05, G:0.11, T:0.26
Consensus pattern (43 bp):
AGTCTCAATTATAAAAGTAAAAAATGAGATTAAAAAAATTAAA
Found at i:56501 original size:21 final size:21
Alignment explanation
Indices: 56475--56535 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
56465 TTAAGAGCTT
56475 TAATTATAAAAGTAAAAAGTGA
1 TAATTATAAAAGTAAAAAGT-A
* * * *
56497 T-ATTAAAAAAATTAAAAGTC
1 TAATTATAAAAGTAAAAAGTA
56517 TCAATTATAAAAGTAAAAA
1 T-AATTATAAAAGTAAAAA
56536 AATACGATTG
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
20 1 0.03
21 15 0.50
22 14 0.47
ACGTcount: A:0.61, C:0.03, G:0.08, T:0.28
Consensus pattern (21 bp):
TAATTATAAAAGTAAAAAGTA
Found at i:67845 original size:5 final size:5
Alignment explanation
Indices: 67830--67915 Score: 90
Period size: 5 Copynumber: 17.2 Consensus size: 5
67820 CAATTTAGTC
67830 TTAATT TTAAT TTAAT TTAA- -TAATT TTAATT TTAAT TTAAT TTAA-
1 TTAA-T TTAAT TTAAT TTAAT TTAA-T TTAA-T TTAAT TTAAT TTAAT
* *
67875 TAAAT TTAATT TTAAT TTAAT TTAA- TAAAT TTAAT TTAAT T
1 TTAAT TTAA-T TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT T
67916 ATTTAATCGA
Statistics
Matches: 70, Mismatches: 4, Indels: 13
0.80 0.05 0.15
Matches are distributed among these distances:
3 3 0.04
4 6 0.09
5 43 0.61
6 18 0.26
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
TTAAT
Found at i:67858 original size:25 final size:25
Alignment explanation
Indices: 67830--67922 Score: 156
Period size: 25 Copynumber: 3.8 Consensus size: 25
67820 CAATTTAGTC
*
67830 TTAATTTTAATTTAATTTAATAATT
1 TTAATTTTAATTTAATTTAATAAAT
67855 TTAATTTTAATTTAATTTAATAAAT
1 TTAATTTTAATTTAATTTAATAAAT
67880 TTAATTTTAATTTAATTTAATAAAT
1 TTAATTTTAATTTAATTTAATAAAT
67905 TTAA-TTTAA-TT-ATTTAAT
1 TTAATTTTAATTTAATTTAAT
67923 CGACATGTGT
Statistics
Matches: 67, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
22 7 0.10
23 2 0.03
24 5 0.07
25 53 0.79
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (25 bp):
TTAATTTTAATTTAATTTAATAAAT
Found at i:73516 original size:15 final size:15
Alignment explanation
Indices: 73473--73518 Score: 55
Period size: 14 Copynumber: 3.3 Consensus size: 15
73463 TCTTTATATA
73473 AATTTAAATATT-TTT
1 AATTTAAA-ATTATTT
73488 AA--TAAAATTA-TT
1 AATTTAAAATTATTT
73500 AATTTAAAATTATTT
1 AATTTAAAATTATTT
73515 AATT
1 AATT
73519 ATGTTTCAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
12 7 0.26
13 4 0.15
14 8 0.30
15 8 0.30
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
AATTTAAAATTATTT
Found at i:73620 original size:2 final size:2
Alignment explanation
Indices: 73615--73672 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
73605 AAATCTAACA
73615 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
73657 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
73673 TATTGTCCTC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:75501 original size:5 final size:5
Alignment explanation
Indices: 75491--75548 Score: 62
Period size: 5 Copynumber: 10.8 Consensus size: 5
75481 AACGGTCAAC
* *
75491 GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTCAAT GGTCG
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG
75540 GGTCG GGTC
1 GGTCG GGTC
75549 AAACCGGTCA
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
5 37 0.82
7 8 0.18
ACGTcount: A:0.07, C:0.21, G:0.52, T:0.21
Consensus pattern (5 bp):
GGTCG
Found at i:75512 original size:22 final size:22
Alignment explanation
Indices: 75484--75548 Score: 121
Period size: 22 Copynumber: 3.0 Consensus size: 22
75474 AATGGTCAAC
75484 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
75506 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
*
75528 GGTCAATGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
75549 AAACCGGTCA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.09, C:0.22, G:0.49, T:0.20
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:75538 original size:17 final size:17
Alignment explanation
Indices: 75518--75550 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
75508 TCAACGGTCG
75518 GGTCGGGTCGGGTCAAT
1 GGTCGGGTCGGGTCAAT
75535 GGTCGGGTCGGGTCAA
1 GGTCGGGTCGGGTCAA
75551 ACCGGTCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.12, C:0.18, G:0.48, T:0.21
Consensus pattern (17 bp):
GGTCGGGTCGGGTCAAT
Found at i:75592 original size:19 final size:19
Alignment explanation
Indices: 75550--75614 Score: 71
Period size: 19 Copynumber: 3.4 Consensus size: 19
75540 GGTCGGGTCA
*
75550 AACCGGTCAAACCGATTC-
1 AACCGGTCAAACCGGTTCG
75568 AGACCGGTCAAACCGGTTCG
1 A-ACCGGTCAAACCGGTTCG
*
75588 AACCGGTTGAAACCGG-TCAG
1 AACCGG-TCAAACCGGTTC-G
75608 AACCGGT
1 AACCGGT
75615 TGAAAACCGG
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
18 1 0.02
19 24 0.59
20 16 0.39
ACGTcount: A:0.29, C:0.29, G:0.26, T:0.15
Consensus pattern (19 bp):
AACCGGTCAAACCGGTTCG
Found at i:75635 original size:9 final size:10
Alignment explanation
Indices: 75547--75635 Score: 87
Period size: 10 Copynumber: 9.1 Consensus size: 10
75537 TCGGGTCGGG
75547 TCAAACCGG-
1 TCAAACCGGT
*
75556 TCAAACCGAT
1 TCAAACCGGT
*
75566 TCAGACCGG-
1 TCAAACCGGT
75575 TCAAACCGGT
1 TCAAACCGGT
*
75585 TCGAACCGGT
1 TCAAACCGGT
*
75595 TGAAACCGG-
1 TCAAACCGGT
75604 TCAGAACCGGT
1 TCA-AACCGGT
*
75615 TGAAAACCGGT
1 T-CAAACCGGT
75626 T-AAACCGGT
1 TCAAACCGGT
75635 T
1 T
75636 TCCAGCAGCC
Statistics
Matches: 66, Mismatches: 9, Indels: 10
0.78 0.11 0.12
Matches are distributed among these distances:
9 27 0.41
10 29 0.44
11 9 0.14
12 1 0.02
ACGTcount: A:0.30, C:0.27, G:0.25, T:0.18
Consensus pattern (10 bp):
TCAAACCGGT
Found at i:82816 original size:5 final size:5
Alignment explanation
Indices: 82806--82880 Score: 69
Period size: 5 Copynumber: 13.8 Consensus size: 5
82796 AACAGTCAAC
* *
82806 GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTCAAC GGTCG
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG
*
82855 GGTCG GGTCAAC GGTCG GGTCG GGTC
1 GGTCG GGTC--G GGTCG GGTCG GGTC
82881 AAACCGGTCA
Statistics
Matches: 58, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
5 46 0.79
7 12 0.21
ACGTcount: A:0.08, C:0.23, G:0.51, T:0.19
Consensus pattern (5 bp):
GGTCG
Found at i:82833 original size:17 final size:17
Alignment explanation
Indices: 82833--82882 Score: 100
Period size: 17 Copynumber: 2.9 Consensus size: 17
82823 TCAACGGTCG
82833 GGTCGGGTCGGGTCAAC
1 GGTCGGGTCGGGTCAAC
82850 GGTCGGGTCGGGTCAAC
1 GGTCGGGTCGGGTCAAC
82867 GGTCGGGTCGGGTCAA
1 GGTCGGGTCGGGTCAA
82883 ACCGGTCAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 33 1.00
ACGTcount: A:0.12, C:0.22, G:0.48, T:0.18
Consensus pattern (17 bp):
GGTCGGGTCGGGTCAAC
Found at i:82876 original size:22 final size:22
Alignment explanation
Indices: 82800--82863 Score: 128
Period size: 22 Copynumber: 2.9 Consensus size: 22
82790 ACGGTCAACA
82800 GTCAACGGTCGGGTCGGGTCGG
1 GTCAACGGTCGGGTCGGGTCGG
82822 GTCAACGGTCGGGTCGGGTCGG
1 GTCAACGGTCGGGTCGGGTCGG
82844 GTCAACGGTCGGGTCGGGTC
1 GTCAACGGTCGGGTCGGGTC
82864 AACGGTCGGG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.09, C:0.23, G:0.48, T:0.19
Consensus pattern (22 bp):
GTCAACGGTCGGGTCGGGTCGG
Found at i:82891 original size:9 final size:9
Alignment explanation
Indices: 82877--82975 Score: 90
Period size: 9 Copynumber: 10.3 Consensus size: 9
82867 GGTCGGGTCG
82877 GGTCAAACC
1 GGTCAAACC
82886 GGTCAAACC
1 GGTCAAACC
* *
82895 GATTCAGACC
1 G-GTCAAACC
82905 GGTCAAACC
1 GGTCAAACC
*
82914 GGTTCGAACC
1 GG-TCAAACC
*
82924 GGTTGAAACC
1 GG-TCAAACC
82934 GGTCAAACC
1 GGTCAAACC
82943 GGTCAGAACC
1 GGTCA-AACC
*
82953 GGTTGAAAACC
1 GG-T-CAAACC
*
82964 GGTTAAACC
1 GGTCAAACC
82973 GGT
1 GGT
82976 TTCCAGCAGC
Statistics
Matches: 75, Mismatches: 10, Indels: 10
0.79 0.11 0.11
Matches are distributed among these distances:
9 37 0.49
10 30 0.40
11 7 0.09
12 1 0.01
ACGTcount: A:0.30, C:0.27, G:0.26, T:0.16
Consensus pattern (9 bp):
GGTCAAACC
Found at i:82934 original size:29 final size:28
Alignment explanation
Indices: 82878--82975 Score: 124
Period size: 29 Copynumber: 3.4 Consensus size: 28
82868 GTCGGGTCGG
* * *
82878 GTCAAACCGGTCAAACCGATTCAGACCG
1 GTCAAACCGGTCAAACCGGTTGAAACCG
*
82906 GTCAAACCGGTTCGAACCGGTTGAAACCG
1 GTCAAACCGG-TCAAACCGGTTGAAACCG
82935 GTCAAACCGGTCAGAACCGGTTGAAAACCG
1 GTCAAACCGGTCA-AACCGGTTG-AAACCG
*
82965 GTTAAACCGGT
1 GTCAAACCGGT
82976 TTCCAGCAGC
Statistics
Matches: 61, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
28 12 0.20
29 33 0.54
30 16 0.26
ACGTcount: A:0.31, C:0.28, G:0.26, T:0.16
Consensus pattern (28 bp):
GTCAAACCGGTCAAACCGGTTGAAACCG
Found at i:82954 original size:19 final size:18
Alignment explanation
Indices: 82877--82975 Score: 90
Period size: 19 Copynumber: 5.2 Consensus size: 18
82867 GGTCGGGTCG
82877 GGTCAAACCGGTCAAACC
1 GGTCAAACCGGTCAAACC
* *
82895 GATTCAGACCGGTCAAACC
1 G-GTCAAACCGGTCAAACC
* *
82914 GGTTCGAACCGGTTGAAACC
1 GG-TCAAACCGG-TCAAACC
82934 GGTCAAACCGGTCAGAACC
1 GGTCAAACCGGTCA-AACC
* *
82953 GGTTGAAAACCGGTTAAACC
1 GG-T-CAAACCGGTCAAACC
82973 GGT
1 GGT
82976 TTCCAGCAGC
Statistics
Matches: 65, Mismatches: 10, Indels: 11
0.76 0.12 0.13
Matches are distributed among these distances:
18 3 0.05
19 38 0.58
20 15 0.23
21 9 0.14
ACGTcount: A:0.30, C:0.27, G:0.26, T:0.16
Consensus pattern (18 bp):
GGTCAAACCGGTCAAACC
Found at i:87213 original size:26 final size:26
Alignment explanation
Indices: 87176--87225 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
87166 TGAATTATAC
87176 TTTACAAATGTTAAATTATTTTTAGT
1 TTTACAAATGTTAAATTATTTTTAGT
* *
87202 TTTA-AAATTGTTTATTTATTTTTA
1 TTTACAAA-TGTTAAATTATTTTTA
87226 ATTAATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 3 0.14
26 18 0.86
ACGTcount: A:0.32, C:0.02, G:0.06, T:0.60
Consensus pattern (26 bp):
TTTACAAATGTTAAATTATTTTTAGT
Found at i:91417 original size:14 final size:14
Alignment explanation
Indices: 91398--91425 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
91388 ATCATAACAA
91398 AATTATATAACTAT
1 AATTATATAACTAT
91412 AATTATATAACTAT
1 AATTATATAACTAT
91426 TCTTTCACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
AATTATATAACTAT
Found at i:91697 original size:9 final size:10
Alignment explanation
Indices: 91670--91708 Score: 60
Period size: 10 Copynumber: 3.9 Consensus size: 10
91660 AACAAAAATC
*
91670 CCGGTTTTTC
1 CCGGTTTTTT
91680 CCGGTTTTTT
1 CCGGTTTTTT
*
91690 CTGGTTTTTT
1 CCGGTTTTTT
91700 CCGGTTTTT
1 CCGGTTTTT
91709 GGACGGTCCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.00, C:0.21, G:0.21, T:0.59
Consensus pattern (10 bp):
CCGGTTTTTT
Found at i:91980 original size:16 final size:17
Alignment explanation
Indices: 91948--91999 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
91938 CACATAAGTA
91948 AATATGTTTAATAAAAT
1 AATATGTTTAATAAAAT
*
91965 AATATGTTT-TTAAAAT
1 AATATGTTTAATAAAAT
* *
91981 -ATATATTTATATAACAT
1 AATATGTTTA-ATAAAAT
91998 AA
1 AA
92000 AAGGTAAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
15 7 0.25
16 6 0.21
17 14 0.50
18 1 0.04
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (17 bp):
AATATGTTTAATAAAAT
Found at i:106306 original size:51 final size:51
Alignment explanation
Indices: 106182--106589 Score: 545
Period size: 51 Copynumber: 8.0 Consensus size: 51
106172 GGCGCAGACA
** * *
106182 CAGCAAGGTGGAAAC-TCAGAGTCCCAAACATATACTCAACTACCTCAACAG
1 CAGCAAGGTGGAAACATTGGA-TCCCAAACATATACTCAGCTACCACAACAG
* * ***
106233 CA-CAAGGTGGAAACTTTGGATCCCAAACATATAGTCAGCTATGGCAACAG
1 CAGCAAGGTGGAAACATTGGATCCCAAACATATACTCAGCTACCACAACAG
* * * * *
106283 CAGCAAGGTGGAAACTTTGGATCCCAGACGTATAGTCAGCTACCGCAACAG
1 CAGCAAGGTGGAAACATTGGATCCCAAACATATACTCAGCTACCACAACAG
* *
106334 CAGCAAGGTGGAAACATTGGATCCCAAACATATACTAATCTACCACAACAG
1 CAGCAAGGTGGAAACATTGGATCCCAAACATATACTCAGCTACCACAACAG
* *
106385 CAGCAAGGTGGAAACATT-GATACCCAAACATATACTCTGCTACCACATCAG
1 CAGCAAGGTGGAAACATTGGAT-CCCAAACATATACTCAGCTACCACAACAG
*
106436 CAGCAAGGTGGAAACAATGGATCCCAAACATATACTCAGCTACCACAACAG
1 CAGCAAGGTGGAAACATTGGATCCCAAACATATACTCAGCTACCACAACAG
* * *
106487 CAGCAAGGTGGAAACATT-GATTCCCAAACATTTACTCTGTTACCACAACAG
1 CAGCAAGGTGGAAACATTGGA-TCCCAAACATATACTCAGCTACCACAACAG
* *
106538 CAGCAAGGTGGAAACATTGGTTCCCAAACATATACTCAGCTACCACAGCAG
1 CAGCAAGGTGGAAACATTGGATCCCAAACATATACTCAGCTACCACAACAG
106589 C
1 C
106590 TCTTAATGTC
Statistics
Matches: 317, Mismatches: 34, Indels: 12
0.87 0.09 0.03
Matches are distributed among these distances:
50 44 0.14
51 269 0.85
52 4 0.01
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.18
Consensus pattern (51 bp):
CAGCAAGGTGGAAACATTGGATCCCAAACATATACTCAGCTACCACAACAG
Done.