Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003982.1 Hibiscus syriacus cultivar Beakdansim tig00008653_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: 70727
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1611 original size:16 final size:16
Alignment explanation
Indices: 1593--1626 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1583 AATATTTATG
1593 AAATATATATTAATAGA
1 AAATAT-TATTAATAGA
*
1610 AAATATTTTTAATAGA
1 AAATATTATTAATAGA
1626 A
1 A
1627 TATGATTGAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (16 bp):
AAATATTATTAATAGA
Found at i:19245 original size:31 final size:28
Alignment explanation
Indices: 19202--19284 Score: 87
Period size: 31 Copynumber: 2.9 Consensus size: 28
19192 TATTTTTTTT
*
19202 TTTTTGTAAAAATAAGTACCTAAAGTTATC
1 TTTTTGTCAAAATAAGTACCTAAAG-TA-C
* *
19232 TTTTTGGTCAAAATAACTACTTAAAGTAC
1 TTTTT-GTCAAAATAAGTACCTAAAGTAC
*
19261 TTTATGTCAAAAT-AGTTACCTAAA
1 TTTTTGTCAAAATAAG-TACCTAAA
19285 CTATTCAAAC
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
27 1 0.02
28 15 0.33
29 5 0.11
30 7 0.16
31 17 0.38
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.39
Consensus pattern (28 bp):
TTTTTGTCAAAATAAGTACCTAAAGTAC
Found at i:19284 original size:28 final size:30
Alignment explanation
Indices: 19210--19284 Score: 75
Period size: 28 Copynumber: 2.5 Consensus size: 30
19200 TTTTTTTGTA
*
19210 AAAATAAGTACCTAAAGTTATCTTTTTGGTC
1 AAAAT-AGTACCTAAAGTTATCTTTATGGTC
* *
19241 AAAATAACTACTTAAAG-TA-CTTTAT-GTC
1 AAAAT-AGTACCTAAAGTTATCTTTATGGTC
19269 AAAATAGTTACCTAAA
1 AAAATAG-TACCTAAA
19285 CTATTCAAAC
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
27 1 0.03
28 15 0.39
29 5 0.13
30 2 0.05
31 15 0.39
ACGTcount: A:0.43, C:0.13, G:0.09, T:0.35
Consensus pattern (30 bp):
AAAATAGTACCTAAAGTTATCTTTATGGTC
Found at i:25590 original size:21 final size:21
Alignment explanation
Indices: 25566--25630 Score: 85
Period size: 21 Copynumber: 3.1 Consensus size: 21
25556 GATATGACAA
*
25566 TTCACGGTACTGAAGTGGCGG
1 TTCACGGTACTGAAGTGGCAG
*
25587 TTCATGGTACTGAAGTGGCAG
1 TTCACGGTACTGAAGTGGCAG
* * *
25608 TTCACGATACTGACGTGGTAG
1 TTCACGGTACTGAAGTGGCAG
25629 TT
1 TT
25631 TAGGGTGGCA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.22, C:0.17, G:0.32, T:0.29
Consensus pattern (21 bp):
TTCACGGTACTGAAGTGGCAG
Found at i:35467 original size:18 final size:18
Alignment explanation
Indices: 35441--35476 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
35431 AACATTGTAT
*
35441 TCCAATGCTTCTGGCAAC
1 TCCAATGCTCCTGGCAAC
*
35459 TCCAGTGCTCCTGGCAAC
1 TCCAATGCTCCTGGCAAC
35477 CGTCGAAGGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.19, C:0.36, G:0.19, T:0.25
Consensus pattern (18 bp):
TCCAATGCTCCTGGCAAC
Found at i:38438 original size:34 final size:32
Alignment explanation
Indices: 38385--38454 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
38375 ACCTTACAAC
*
38385 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
*
38417 TCCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAGAACCTT
38451 TCCC
1 TCCC
38455 CTTTACAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 22 0.65
ACGTcount: A:0.21, C:0.31, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
Found at i:38694 original size:20 final size:22
Alignment explanation
Indices: 38669--38708 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
38659 AGTCGTATAT
38669 AGCCG-TTGGGGATG-TTTTGA
1 AGCCGTTTGGGGATGATTTTGA
38689 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
38709 TATACTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.15, C:0.10, G:0.38, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGA
Found at i:38761 original size:21 final size:21
Alignment explanation
Indices: 38737--38779 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
38727 CCCAGAATAG
*
38737 AGGGAATCGGTACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
38758 AGGGAATCGATACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
38779 A
1 A
38780 ATATTCAAAT
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:0.21, T:0.23
Consensus pattern (21 bp):
AGGGAATCGATACCCCTTCAT
Found at i:38841 original size:21 final size:21
Alignment explanation
Indices: 38815--38857 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
38805 CTGTTGAACA
38815 GGGGGGAATCGGTACCCCCTG
1 GGGGGGAATCGGTACCCCCTG
38836 GGGGGGAATCGGTACCCCCTG
1 GGGGGGAATCGGTACCCCCTG
38857 G
1 G
38858 ACATTCTGTT
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:0.14, C:0.28, G:0.44, T:0.14
Consensus pattern (21 bp):
GGGGGGAATCGGTACCCCCTG
Found at i:38916 original size:21 final size:21
Alignment explanation
Indices: 38891--38970 Score: 91
Period size: 21 Copynumber: 4.0 Consensus size: 21
38881 AAAACCTGCA
38891 GGGGGTATCTGTACCCCCTGGG
1 GGGGGTATCTGTACCCCCT-GG
38913 GGGGGTATCTGTA--CCC---
1 GGGGGTATCTGTACCCCCTGG
38929 -GGGGTATCTGTACCCCCTGG
1 GGGGGTATCTGTACCCCCTGG
* *
38949 GGGGGAATCTATACCCCCTGG
1 GGGGGTATCTGTACCCCCTGG
38970 G
1 G
38971 CAATCTTGAA
Statistics
Matches: 50, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
15 12 0.24
17 3 0.06
20 3 0.06
21 19 0.38
22 13 0.26
ACGTcount: A:0.12, C:0.28, G:0.38, T:0.23
Consensus pattern (21 bp):
GGGGGTATCTGTACCCCCTGG
Found at i:38934 original size:15 final size:15
Alignment explanation
Indices: 38914--38943 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
38904 CCCCCTGGGG
38914 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
38929 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
38944 CCTGGGGGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.33, T:0.27
Consensus pattern (15 bp):
GGGGTATCTGTACCC
Found at i:38964 original size:36 final size:37
Alignment explanation
Indices: 38892--38964 Score: 121
Period size: 37 Copynumber: 2.0 Consensus size: 37
38882 AAACCTGCAG
* *
38892 GGGGTATCTGTACCCCCTGGGGGGGGTATCTGTACCC
1 GGGGTATCTGTACCCCCTGGGGGGGGAATCTATACCC
38929 GGGGTATCTGTACCCCCT-GGGGGGGAATCTATACCC
1 GGGGTATCTGTACCCCCTGGGGGGGGAATCTATACCC
38965 CCTGGGCAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
36 16 0.47
37 18 0.53
ACGTcount: A:0.14, C:0.27, G:0.36, T:0.23
Consensus pattern (37 bp):
GGGGTATCTGTACCCCCTGGGGGGGGAATCTATACCC
Found at i:39092 original size:29 final size:31
Alignment explanation
Indices: 39060--39119 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
39050 AAACTTTGAA
*
39060 TAAATTCAATT-ACGTCCAAAAA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
39089 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
39120 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 10 0.36
31 7 0.25
ACGTcount: A:0.42, C:0.18, G:0.07, T:0.33
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:40430 original size:19 final size:20
Alignment explanation
Indices: 40387--40434 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
40377 TTTAAATCCT
*
40387 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
40407 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
40426 TTTTCAAAA
1 TTTTCAAAA
40435 GAAAATCGTT
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:41649 original size:21 final size:21
Alignment explanation
Indices: 41625--41667 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
41615 CCCAGAATAG
*
41625 AGGGAATCGGTACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
41646 AGGGAATCGATACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
41667 A
1 A
41668 ATATTCAAAT
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:0.21, T:0.23
Consensus pattern (21 bp):
AGGGAATCGATACCCCTTCAT
Found at i:41729 original size:21 final size:21
Alignment explanation
Indices: 41703--41746 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
41693 CTGTTGAACA
41703 GGGGGGGAATCGGTACCCCCT
1 GGGGGGGAATCGGTACCCCCT
41724 GGGGGGGAATCGGTACCCCCT
1 GGGGGGGAATCGGTACCCCCT
41745 GG
1 GG
41747 ACATTCTGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.14, C:0.27, G:0.45, T:0.14
Consensus pattern (21 bp):
GGGGGGGAATCGGTACCCCCT
Found at i:41805 original size:21 final size:21
Alignment explanation
Indices: 41780--41859 Score: 73
Period size: 21 Copynumber: 4.0 Consensus size: 21
41770 AAAACCTGCA
41780 GGGGGTATCTGTACCCCCTGGG
1 GGGGGTATCTGTACCCCCT-GG
41802 GGGGGTATCTGTA--CCC---
1 GGGGGTATCTGTACCCCCTGG
*
41818 -AGGGTATCTGTACCCCCTGG
1 GGGGGTATCTGTACCCCCTGG
* * *
41838 GGGTGAATCTATACCCCCTGG
1 GGGGGTATCTGTACCCCCTGG
41859 G
1 G
41860 CAATCTTGAA
Statistics
Matches: 47, Mismatches: 5, Indels: 13
0.72 0.08 0.20
Matches are distributed among these distances:
15 11 0.23
17 3 0.06
20 3 0.06
21 17 0.36
22 13 0.28
ACGTcount: A:0.14, C:0.28, G:0.35, T:0.24
Consensus pattern (21 bp):
GGGGGTATCTGTACCCCCTGG
Found at i:41824 original size:15 final size:15
Alignment explanation
Indices: 41804--41832 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
41794 CCCCTGGGGG
41804 GGGTATCTGTACCCA
1 GGGTATCTGTACCCA
41819 GGGTATCTGTACCC
1 GGGTATCTGTACCC
41833 CCTGGGGGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.28, G:0.28, T:0.28
Consensus pattern (15 bp):
GGGTATCTGTACCCA
Found at i:41853 original size:36 final size:37
Alignment explanation
Indices: 41782--41853 Score: 110
Period size: 37 Copynumber: 2.0 Consensus size: 37
41772 AACCTGCAGG
* *
41782 GGGTATCTGTACCCCCTGGGGGGGGTATCTGTACCCA
1 GGGTATCTGTACCCCCTGGGGGGGGAATCTATACCCA
*
41819 GGGTATCTGTACCCCCT-GGGGGTGAATCTATACCC
1 GGGTATCTGTACCCCCTGGGGGGGGAATCTATACCC
41854 CCTGGGCAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
36 15 0.47
37 17 0.53
ACGTcount: A:0.15, C:0.28, G:0.32, T:0.25
Consensus pattern (37 bp):
GGGTATCTGTACCCCCTGGGGGGGGAATCTATACCCA
Found at i:41981 original size:29 final size:31
Alignment explanation
Indices: 41949--42008 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
41939 AAACTTTGAA
*
41949 TAAATTCAATT-ACGTCCAAAAA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
41978 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
42009 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 10 0.36
31 7 0.25
ACGTcount: A:0.42, C:0.18, G:0.07, T:0.33
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:45305 original size:29 final size:29
Alignment explanation
Indices: 45259--45338 Score: 103
Period size: 29 Copynumber: 2.8 Consensus size: 29
45249 AATACGTATA
45259 ATATATTTATTTTAAAAACTATATA-AC-
1 ATATATTTATTTTAAAAACTATATATACT
*
45286 ATATATTATATTTTCAAAAATTATATATACT
1 ATATATT-TATTTT-AAAAACTATATATACT
45317 ATATATGTT-TTTTAAAAACTAT
1 ATATAT-TTATTTTAAAAACTAT
45339 TTTCAAAATT
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
27 7 0.15
28 6 0.13
29 19 0.41
30 6 0.13
31 7 0.15
32 1 0.02
ACGTcount: A:0.45, C:0.06, G:0.01, T:0.47
Consensus pattern (29 bp):
ATATATTTATTTTAAAAACTATATATACT
Found at i:45343 original size:42 final size:38
Alignment explanation
Indices: 45294--45376 Score: 114
Period size: 42 Copynumber: 2.1 Consensus size: 38
45284 ACATATATTA
45294 TATTTTCAAAAATT-ATATATACTATATATGTTTTTTAAAAAC
1 TATTTTC-AAAATTCATATATA-T-TATATG-TTTTT-AAAAC
45336 TATTTTCAAAATTCATATATATTATATGTTTTTAAAAC
1 TATTTTCAAAATTCATATATATTATATGTTTTTAAAAC
45374 TAT
1 TAT
45377 AAAATATATT
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
38 8 0.20
39 5 0.12
40 6 0.15
41 7 0.17
42 14 0.35
ACGTcount: A:0.41, C:0.07, G:0.02, T:0.49
Consensus pattern (38 bp):
TATTTTCAAAATTCATATATATTATATGTTTTTAAAAC
Found at i:45354 original size:40 final size:40
Alignment explanation
Indices: 45294--45376 Score: 109
Period size: 40 Copynumber: 2.1 Consensus size: 40
45284 ACATATATTA
*
45294 TATTTTCAAAAATTATATATACTA-TATATGTTTTTTAAAAAC
1 TATTTTCAAAAATTACATATA-TATTATATG-TTTTT-AAAAC
45336 TATTTTC-AAAATT-CATATATATTATATGTTTTTAAAAC
1 TATTTTCAAAAATTACATATATATTATATGTTTTTAAAAC
45374 TAT
1 TAT
45377 AAAATATATT
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
38 8 0.21
39 7 0.18
40 11 0.28
41 6 0.15
42 7 0.18
ACGTcount: A:0.41, C:0.07, G:0.02, T:0.49
Consensus pattern (40 bp):
TATTTTCAAAAATTACATATATATTATATGTTTTTAAAAC
Found at i:45417 original size:17 final size:17
Alignment explanation
Indices: 45380--45420 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
45370 AAACTATAAA
**
45380 ATATATTTTCAAAAATT
1 ATATATTTTCAAAAACC
45397 ATATATTTTCAAAAACC
1 ATATATTTTCAAAAACC
45414 ATATATT
1 ATATATT
45421 ATATACAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.46, C:0.10, G:0.00, T:0.44
Consensus pattern (17 bp):
ATATATTTTCAAAAACC
Found at i:49115 original size:14 final size:14
Alignment explanation
Indices: 49096--49130 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
49086 CTATACCGGT
49096 TGAACCGCTACTAG
1 TGAACCGCTACTAG
49110 TGAACCGCTACTAG
1 TGAACCGCTACTAG
49124 TGAACCG
1 TGAACCG
49131 GTCGAACCGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.29, C:0.29, G:0.23, T:0.20
Consensus pattern (14 bp):
TGAACCGCTACTAG
Found at i:49720 original size:14 final size:14
Alignment explanation
Indices: 49684--49710 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
49674 ATTTATTTTT
49684 TAATTATATTTATA
1 TAATTATATTTATA
49698 TAATTATATTTAT
1 TAATTATATTTAT
49711 TATTTAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TAATTATATTTATA
Found at i:52323 original size:21 final size:21
Alignment explanation
Indices: 52299--52339 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
52289 GATAAAAAAT
*
52299 TACCTAAAACATTATTATTTC
1 TACCTAAAACATTAATATTTC
52320 TACCTAAAACATTAATATTT
1 TACCTAAAACATTAATATTT
52340 TTTAACAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.41, C:0.17, G:0.00, T:0.41
Consensus pattern (21 bp):
TACCTAAAACATTAATATTTC
Found at i:60512 original size:3 final size:3
Alignment explanation
Indices: 60498--60581 Score: 132
Period size: 3 Copynumber: 27.3 Consensus size: 3
60488 GTTTAAAAAA
60498 TAT TAT TAAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
60544 TAA TAT TAT TAT TAA TAT TAT TAT TAT TAAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT T
60582 TACCACTACC
Statistics
Matches: 75, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
3 69 0.92
4 6 0.08
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:63564 original size:8 final size:8
Alignment explanation
Indices: 63522--63563 Score: 70
Period size: 8 Copynumber: 5.5 Consensus size: 8
63512 ATTTTATTAC
63522 TTTTAAAA
1 TTTTAAAA
63530 TTTTAAAA
1 TTTTAAAA
63538 TTTTAAAA
1 TTTTAAAA
63546 TTTT-AAA
1 TTTTAAAA
63553 TTTT-AAA
1 TTTTAAAA
63560 TTTT
1 TTTT
63564 TTTTTATTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
7 14 0.41
8 20 0.59
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (8 bp):
TTTTAAAA
Found at i:63565 original size:16 final size:15
Alignment explanation
Indices: 63522--63564 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
63512 ATTTTATTAC
*
63522 TTTTAAAATTTTAAAA
1 TTTT-AAATTTTTAAA
*
63538 TTTTAAAATTTTAAA
1 TTTTAAATTTTTAAA
63553 TTTTAAATTTTT
1 TTTTAAATTTTT
63565 TTTTATTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
15 20 0.83
16 4 0.17
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTTTAAATTTTTAAA
Found at i:63600 original size:11 final size:11
Alignment explanation
Indices: 63584--63609 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
63574 TTTCCATTTG
63584 ATTTATTTAAT
1 ATTTATTTAAT
63595 ATTTATTTAAT
1 ATTTATTTAAT
63606 ATTT
1 ATTT
63610 CTTATCTAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
ATTTATTTAAT
Found at i:66353 original size:18 final size:17
Alignment explanation
Indices: 66332--66365 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
66322 TTTTTATGAT
*
66332 TTTTGTTTTTTTACTTTC
1 TTTTGTTATTTT-CTTTC
66350 TTTTGTTATTTTCTTT
1 TTTTGTTATTTTCTTT
66366 TTCTTTTCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.06, C:0.09, G:0.06, T:0.79
Consensus pattern (17 bp):
TTTTGTTATTTTCTTTC
Found at i:66372 original size:11 final size:11
Alignment explanation
Indices: 66358--66382 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
66348 TCTTTTGTTA
66358 TTTTCTTTTTC
1 TTTTCTTTTTC
66369 TTTTCTTTTTC
1 TTTTCTTTTTC
66380 TTT
1 TTT
66383 GTTACATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTCTTTTTC
Done.