Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003353.1 Hibiscus syriacus cultivar Beakdansim tig00007058_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: 72685
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:4215 original size:16 final size:16
Alignment explanation
Indices: 4194--4235 Score: 84
Period size: 16 Copynumber: 2.6 Consensus size: 16
4184 TGCATATATA
4194 AAACTCTCAATCTTTC
1 AAACTCTCAATCTTTC
4210 AAACTCTCAATCTTTC
1 AAACTCTCAATCTTTC
4226 AAACTCTCAA
1 AAACTCTCAA
4236 ACTCTCTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.36, C:0.31, G:0.00, T:0.33
Consensus pattern (16 bp):
AAACTCTCAATCTTTC
Found at i:4219 original size:8 final size:8
Alignment explanation
Indices: 4194--4241 Score: 60
Period size: 8 Copynumber: 6.0 Consensus size: 8
4184 TGCATATATA
4194 AAACTCTC
1 AAACTCTC
* *
4202 AATCTTTC
1 AAACTCTC
4210 AAACTCTC
1 AAACTCTC
* *
4218 AATCTTTC
1 AAACTCTC
4226 AAACTCTC
1 AAACTCTC
4234 AAACTCTC
1 AAACTCTC
4242 TAAATGAAGC
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
8 32 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (8 bp):
AAACTCTC
Found at i:6931 original size:6 final size:6
Alignment explanation
Indices: 6917--6947 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
6907 GAAATATTAT
*
6917 ACCCAA ACCCGA ACCCGA ACCCGA ACCCGA A
1 ACCCGA ACCCGA ACCCGA ACCCGA ACCCGA A
6948 AATATTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.39, C:0.48, G:0.13, T:0.00
Consensus pattern (6 bp):
ACCCGA
Found at i:6986 original size:25 final size:25
Alignment explanation
Indices: 6958--7008 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
6948 AATATTTTAT
6958 ATATAAT-TAATATAAAAAATATAAA
1 ATATAATAT-ATATAAAAAATATAAA
* **
6983 ATATTATATATATAATTAATATAAA
1 ATATAATATATATAAAAAATATAAA
7008 A
1 A
7009 AATATAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 21 0.95
26 1 0.05
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (25 bp):
ATATAATATATATAAAAAATATAAA
Found at i:7026 original size:2 final size:2
Alignment explanation
Indices: 7017--7048 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
7007 AAAATATAAA
7017 AT AT -T 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 AT AT AT A
7049 ATCGGGGCGG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:7049 original size:34 final size:34
Alignment explanation
Indices: 6946--7030 Score: 161
Period size: 34 Copynumber: 2.5 Consensus size: 34
6936 CCCGAACCCG
*
6946 AAAATATTTTATATATAATTAATATAAAAAATAT
1 AAAATATTATATATATAATTAATATAAAAAATAT
6980 AAAATATTATATATATAATTAATATAAAAAATAT
1 AAAATATTATATATATAATTAATATAAAAAATAT
7014 AAAATATTATATATATA
1 AAAATATTATATATATA
7031 TATATATATA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 50 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (34 bp):
AAAATATTATATATATAATTAATATAAAAAATAT
Found at i:7133 original size:42 final size:42
Alignment explanation
Indices: 7074--7169 Score: 192
Period size: 42 Copynumber: 2.3 Consensus size: 42
7064 CCTTGTCTCG
7074 AACCCGACCCGAACAAATCCCCGAAAAATATCTCCGAACCCA
1 AACCCGACCCGAACAAATCCCCGAAAAATATCTCCGAACCCA
7116 AACCCGACCCGAACAAATCCCCGAAAAATATCTCCGAACCCA
1 AACCCGACCCGAACAAATCCCCGAAAAATATCTCCGAACCCA
7158 AACCCGACCCGA
1 AACCCGACCCGA
7170 TATCATTCAA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 54 1.00
ACGTcount: A:0.40, C:0.42, G:0.10, T:0.08
Consensus pattern (42 bp):
AACCCGACCCGAACAAATCCCCGAAAAATATCTCCGAACCCA
Found at i:24293 original size:56 final size:54
Alignment explanation
Indices: 24224--24404 Score: 199
Period size: 56 Copynumber: 3.3 Consensus size: 54
24214 CACTGTTTTC
* *
24224 TAGATATATTCGATTTCGGAGCCATTATTTTTATACTTCTTAATGGAAACAACTGA
1 TAGATATACTCGATTTCGGAGCC-TTATTTTTATGCTTCTTAATGG-AACAACTGA
**
24280 TAGATATACTCGATTT-TTAGGCCTCTATTTTTATGCTTCTTAATGGCAACAACTGA
1 TAGATATACTCGATTTCGGA-GCCT-TATTTTTATGCTTCTTAATGG-AACAACTGA
** * * *
24336 TAGATATACTTTATTTCGGAAGCCCTATTTTTATGCTTATTAAT-G-ACAACTAA
1 TAGATATACTCGATTTCGG-AGCCTTATTTTTATGCTTCTTAATGGAACAACTGA
24389 TA-ATATACTCGATTTC
1 TAGATATACTCGATTTC
24405 AGACCCCTTT
Statistics
Matches: 107, Mismatches: 14, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
52 12 0.11
53 9 0.08
55 3 0.03
56 79 0.74
57 3 0.03
58 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.13, T:0.41
Consensus pattern (54 bp):
TAGATATACTCGATTTCGGAGCCTTATTTTTATGCTTCTTAATGGAACAACTGA
Found at i:27234 original size:54 final size:54
Alignment explanation
Indices: 27150--27544 Score: 495
Period size: 54 Copynumber: 7.3 Consensus size: 54
27140 TTATATTAGT
* *
27150 ACTATGTGTGCAACCCAC-ATAATTCATAATAAGTTTATGAACGACCATATCGAC
1 ACTATGTGTGCAACCCACGA-AATTCATAATAAGTTTATGAACGACCGTATCGGC
* * * * *
27204 ATTATGTGTGCAACCCACGAAATTCATAATAAGTTTATGAATGACTGTATTGAC
1 ACTATGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGACCGTATCGGC
* * *
27258 ACTATGTGTGTAACCCACGAAATTCATAATAAGTTTATGAACGACAGTATAGGC
1 ACTATGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGACCGTATCGGC
* * * *
27312 AATATGTGTACAACCCACAAAATTCATAATAAGTTTATGAACAACCGTATCGGC
1 ACTATGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGACCGTATCGGC
27366 ACTATGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGACCGTATCGGC
1 ACTATGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGACCGTATCGGC
* * * * **
27420 AATATGTGTGCAACCCACGGAATTCATAACAAGTTTATGAACGATCGTATCGAT
1 ACTATGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGACCGTATCGGC
* * * * * * * * *
27474 ACTATATTTGTAACTCACGGAATTCATAATGAGCTTATGAATGACCATATCGGC
1 ACTATGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGACCGTATCGGC
* *
27528 ACTACGTGTGCACCCCA
1 ACTATGTGTGCAACCCA
27545 AAGAACTTAT
Statistics
Matches: 293, Mismatches: 47, Indels: 2
0.86 0.14 0.01
Matches are distributed among these distances:
54 292 1.00
55 1 0.00
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.28
Consensus pattern (54 bp):
ACTATGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGACCGTATCGGC
Found at i:33180 original size:24 final size:24
Alignment explanation
Indices: 33153--33264 Score: 77
Period size: 24 Copynumber: 4.7 Consensus size: 24
33143 TATATCAAAA
*
33153 ATCAAAACATAAATCAGGTCAAGT
1 ATCAAAACAGAAATCAGGTCAAGT
* *
33177 ATCATATCAGAAATCAGGTCAAGT
1 ATCAAAACAGAAATCAGGTCAAGT
* * * *
33201 AACAGATCAG-AATCCAAGTC-AGAT
1 ATCAAAACAGAAAT-CAGGTCAAG-T
* * *
33225 ATCAGATCAG-AATCCATGTCAAGT
1 ATCAAAACAGAAAT-CAGGTCAAGT
*
33249 ATCAAATCAGAAATCA
1 ATCAAAACAGAAATCA
33265 AATCGAAAAT
Statistics
Matches: 75, Mismatches: 9, Indels: 8
0.82 0.10 0.09
Matches are distributed among these distances:
23 5 0.07
24 65 0.87
25 5 0.07
ACGTcount: A:0.46, C:0.19, G:0.14, T:0.21
Consensus pattern (24 bp):
ATCAAAACAGAAATCAGGTCAAGT
Found at i:34385 original size:18 final size:18
Alignment explanation
Indices: 34362--34397 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
34352 CTTCCATCCG
*
34362 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
34380 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
34398 GTCCTTTCGA
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:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:35719 original size:7 final size:7
Alignment explanation
Indices: 35707--35737 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
35697 TGGTCAACTC
35707 CGGTCAA
1 CGGTCAA
35714 CGGTCAA
1 CGGTCAA
35721 CGGTCAA
1 CGGTCAA
35728 CGGTCAA
1 CGGTCAA
35735 CGG
1 CGG
35738 GTCGGGTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.26, C:0.29, G:0.32, T:0.13
Consensus pattern (7 bp):
CGGTCAA
Found at i:35758 original size:18 final size:18
Alignment explanation
Indices: 35735--35798 Score: 119
Period size: 18 Copynumber: 3.6 Consensus size: 18
35725 CAACGGTCAA
35735 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
35753 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
*
35771 CGGGTCGGGTAAACGGGT
1 CGGGTCGGGTCAACGGGT
35789 CGGGTCGGGT
1 CGGGTCGGGT
35799 TATGACCGGT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
18 45 1.00
ACGTcount: A:0.11, C:0.20, G:0.52, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:35776 original size:13 final size:13
Alignment explanation
Indices: 35729--35758 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
35719 AACGGTCAAC
35729 GGTCAACGGGTCG
1 GGTCAACGGGTCG
35742 GGTCAACGGGTCG
1 GGTCAACGGGTCG
35755 GGTC
1 GGTC
35759 GGGTCAACGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.13, C:0.23, G:0.47, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:35788 original size:31 final size:29
Alignment explanation
Indices: 35729--35794 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 29
35719 AACGGTCAAC
35729 GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGT--ACGGGTCGGGTCG
35760 GGTCAACGGGTCGGGT-CGGGTAAACGGGTCG
1 GGTCAACGGGTCGGGTACGGGT---CGGGTCG
35791 GGTC
1 GGTC
35795 GGGTTATGAC
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
28 5 0.16
31 27 0.84
ACGTcount: A:0.14, C:0.21, G:0.48, T:0.17
Consensus pattern (29 bp):
GGTCAACGGGTCGGGTACGGGTCGGGTCG
Found at i:37981 original size:24 final size:24
Alignment explanation
Indices: 37954--38065 Score: 77
Period size: 24 Copynumber: 4.7 Consensus size: 24
37944 TATATCAAAA
*
37954 ATCAAAACATAAATCAGGTCAAGT
1 ATCAAAACAGAAATCAGGTCAAGT
* *
37978 ATCATATCAGAAATCAGGTCAAGT
1 ATCAAAACAGAAATCAGGTCAAGT
* * * *
38002 AACAGATCAG-AATCCAAGTC-AGAT
1 ATCAAAACAGAAAT-CAGGTCAAG-T
* * *
38026 ATCAGATCAG-AATCCATGTCAAGT
1 ATCAAAACAGAAAT-CAGGTCAAGT
*
38050 ATCAAATCAGAAATCA
1 ATCAAAACAGAAATCA
38066 AATCGAAAAT
Statistics
Matches: 75, Mismatches: 9, Indels: 8
0.82 0.10 0.09
Matches are distributed among these distances:
23 5 0.07
24 65 0.87
25 5 0.07
ACGTcount: A:0.46, C:0.19, G:0.14, T:0.21
Consensus pattern (24 bp):
ATCAAAACAGAAATCAGGTCAAGT
Found at i:39184 original size:18 final size:18
Alignment explanation
Indices: 39161--39196 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
39151 CTTCCATCCG
*
39161 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
39179 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
39197 GTCCTTTCGA
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:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:40519 original size:7 final size:7
Alignment explanation
Indices: 40507--40545 Score: 60
Period size: 7 Copynumber: 5.4 Consensus size: 7
40497 TGGTCAACTC
40507 CGGTCAA
1 CGGTCAA
40514 CGGTCAA
1 CGGTCAA
40521 CGGGTCAA
1 C-GGTCAA
*
40529 GGGTCAA
1 CGGTCAA
40536 CGGTCAA
1 CGGTCAA
40543 CGG
1 CGG
40546 GTCGGGTCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
7 23 0.79
8 6 0.21
ACGTcount: A:0.26, C:0.26, G:0.36, T:0.13
Consensus pattern (7 bp):
CGGTCAA
Found at i:40528 original size:8 final size:8
Alignment explanation
Indices: 40508--40592 Score: 71
Period size: 8 Copynumber: 11.5 Consensus size: 8
40498 GGTCAACTCC
40508 GGTCAAC-
1 GGTCAACG
40515 GGTCAACG
1 GGTCAACG
40523 GGTCAA-G
1 GGTCAACG
40530 GGTCAAC-
1 GGTCAACG
40537 GGTCAACG
1 GGTCAACG
40545 GGT---CG
1 GGTCAACG
40550 GGTCAACG
1 GGTCAACG
**
40558 GGTCGGGTCG
1 GGTC--AACG
40568 GGTCAACG
1 GGTCAACG
40576 GGT---CG
1 GGTCAACG
40581 GGTCAACG
1 GGTCAACG
40589 GGTC
1 GGTC
40593 GGGTCGGGTA
Statistics
Matches: 63, Mismatches: 4, Indels: 21
0.72 0.05 0.24
Matches are distributed among these distances:
5 10 0.16
7 21 0.33
8 26 0.41
10 6 0.10
ACGTcount: A:0.19, C:0.24, G:0.42, T:0.15
Consensus pattern (8 bp):
GGTCAACG
Found at i:40528 original size:15 final size:15
Alignment explanation
Indices: 40507--40561 Score: 64
Period size: 15 Copynumber: 3.9 Consensus size: 15
40497 TGGTCAACTC
40507 CGGTCAAC-GGTCAA
1 CGGTCAACGGGTCAA
40521 CGGGTCAA-GGGTCAA
1 C-GGTCAACGGGTCAA
40536 CGGTCAACGGGTC--
1 CGGTCAACGGGTCAA
*
40549 GGGTCAACGGGTC
1 CGGTCAACGGGTC
40562 GGGTCGGGTC
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
13 12 0.32
14 7 0.19
15 18 0.49
ACGTcount: A:0.22, C:0.25, G:0.38, T:0.15
Consensus pattern (15 bp):
CGGTCAACGGGTCAA
Found at i:40535 original size:22 final size:20
Alignment explanation
Indices: 40508--40576 Score: 90
Period size: 22 Copynumber: 3.5 Consensus size: 20
40498 GGTCAACTCC
40508 GGTCAACGGTCAACGGGTCAAG
1 GGTCAACGGTCAACGGGTC--G
40530 GGTCAACGGTCAACGGGTCG
1 GGTCAACGGTCAACGGGTCG
40550 GGTCAACGGGT---CGGGTCG
1 GGTCAAC-GGTCAACGGGTCG
40568 GGTCAACGG
1 GGTCAACGG
40577 GTCGGGTCAA
Statistics
Matches: 46, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
17 2 0.04
18 14 0.30
20 8 0.17
21 3 0.07
22 19 0.41
ACGTcount: A:0.20, C:0.23, G:0.42, T:0.14
Consensus pattern (20 bp):
GGTCAACGGTCAACGGGTCG
Found at i:40555 original size:13 final size:13
Alignment explanation
Indices: 40537--40597 Score: 77
Period size: 13 Copynumber: 4.3 Consensus size: 13
40527 AAGGGTCAAC
40537 GGTCAACGGGTCG
1 GGTCAACGGGTCG
40550 GGTCAACGGGTCGGGTCG
1 GGTCAA-----CGGGTCG
40568 GGTCAACGGGTCG
1 GGTCAACGGGTCG
40581 GGTCAACGGGTCG
1 GGTCAACGGGTCG
40594 GGTC
1 GGTC
40598 GGGTAAACAG
Statistics
Matches: 43, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
13 30 0.70
18 13 0.30
ACGTcount: A:0.13, C:0.23, G:0.48, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:40566 original size:18 final size:18
Alignment explanation
Indices: 40543--40616 Score: 95
Period size: 18 Copynumber: 4.4 Consensus size: 18
40533 CAACGGTCAA
40543 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
40561 CGGGTCGGGTCAA-----
1 CGGGTCGGGTCAACGGGT
40574 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
* *
40592 CGGGTCGGGTAAACAGGT
1 CGGGTCGGGTCAACGGGT
40610 CGGGTCG
1 CGGGTCG
40617 AGTTGTGACC
Statistics
Matches: 49, Mismatches: 2, Indels: 10
0.80 0.03 0.16
Matches are distributed among these distances:
13 13 0.27
18 36 0.73
ACGTcount: A:0.14, C:0.22, G:0.49, T:0.16
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:40575 original size:31 final size:31
Alignment explanation
Indices: 40537--40615 Score: 140
Period size: 31 Copynumber: 2.5 Consensus size: 31
40527 AAGGGTCAAC
40537 GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
40568 GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
* *
40599 GGTAAACAGGTCGGGTC
1 GGTCAACGGGTCGGGTC
40616 GAGTTGTGAC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.15, C:0.22, G:0.47, T:0.16
Consensus pattern (31 bp):
GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
Found at i:47149 original size:5 final size:5
Alignment explanation
Indices: 47139--47192 Score: 108
Period size: 5 Copynumber: 10.8 Consensus size: 5
47129 TTGTTGATTG
47139 TGATA TGATA TGATA TGATA TGATA TGATA TGATA TGATA TGATA TGATA
1 TGATA TGATA TGATA TGATA TGATA TGATA TGATA TGATA TGATA TGATA
47189 TGAT
1 TGAT
47193 CCCAAAATCT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 49 1.00
ACGTcount: A:0.39, C:0.00, G:0.20, T:0.41
Consensus pattern (5 bp):
TGATA
Found at i:48696 original size:23 final size:22
Alignment explanation
Indices: 48650--48693 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
48640 TAAACATTTT
48650 TATTTTTTTAATTAAAAAATAA
1 TATTTTTTTAATTAAAAAATAA
48672 TATTTTTATT-ATTAAAAAATAA
1 TATTTTT-TTAATTAAAAAATAA
48694 ATAATAAACA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 19 0.90
23 2 0.10
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
TATTTTTTTAATTAAAAAATAA
Found at i:59323 original size:83 final size:82
Alignment explanation
Indices: 59128--59538 Score: 477
Period size: 83 Copynumber: 5.0 Consensus size: 82
59118 ATAGAATATA
* * *
59128 TGCCTTTCATTTCGGATGGGATGGGACATTATGACATGGCAAAGATTCTCTGAATAATAATGGAA
1 TGCCTTTCATTTCGGATGGGATGGAACACTATGACATGGCAGAGATTCTCTGAATAATAATGGAA
* * *
59193 AATAATTCCCTGTAAC-
66 AACATTTCCCTGGAACG
* * * * *
59209 TCGCCTTTCATTTTGGATGGGATGGAACACTATGACATGGCAGAAATTCACTAAATAATAATGAA
1 T-GCCTTTCATTTCGGATGGGATGGAACACTATGACATGGCAGAGATTCTCTGAATAATAATGGA
59274 AAACATTTCCCCTGGAACG
65 AAACATTT-CCCTGGAACG
* * * *
59293 TGCATTTCATTTCAGAAGGGATGGAACACTATGACAAGGCAGAGATTCTCTGAATAATAATGGAA
1 TGCCTTTCATTTCGGATGGGATGGAACACTATGACATGGCAGAGATTCTCTGAATAATAATGGAA
*
59358 AACACTTTCCCTGGAATG
66 AACA-TTTCCCTGGAACG
** * * * *
59376 TGCCTTTCATTTCGGATGGGATATAATACTTTGACATGGAAGAGATTCTCTTAATAATAATGGAA
1 TGCCTTTCATTTCGGATGGGATGGAACACTATGACATGGCAGAGATTCTCTGAATAATAATGGAA
* *
59441 AACGCTTCCCCTGGAACG
66 AAC-ATTTCCCTGGAACG
* * * * **
59459 TGTCTTTAATTTTGGATGGAATGGAACACTATGACATGGCAGAGATTCTCTGAA-AAT-GGGGAA
1 TGCCTTTCATTTCGGATGGGATGGAACACTATGACATGGCAGAGATTCTCTGAATAATAATGGAA
* *
59522 AACACTTCCCTGAAACG
66 AACATTTCCCTGGAACG
59539 AATCTTTCTT
Statistics
Matches: 275, Mismatches: 50, Indels: 11
0.82 0.15 0.03
Matches are distributed among these distances:
80 10 0.04
81 8 0.03
82 64 0.23
83 189 0.69
84 4 0.01
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (82 bp):
TGCCTTTCATTTCGGATGGGATGGAACACTATGACATGGCAGAGATTCTCTGAATAATAATGGAA
AACATTTCCCTGGAACG
Found at i:60397 original size:26 final size:27
Alignment explanation
Indices: 60362--60413 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 27
60352 TGAACTATAA
*
60362 AAACAACAAACCA-TAAACATTACATT
1 AAACAACAAACCATTAAACATGACATT
*
60388 AAACAACAAACTATTAAACATGACAT
1 AAACAACAAACCATTAAACATGACAT
60414 AAAGCATACC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 12 0.52
27 11 0.48
ACGTcount: A:0.58, C:0.21, G:0.02, T:0.19
Consensus pattern (27 bp):
AAACAACAAACCATTAAACATGACATT
Found at i:60508 original size:32 final size:32
Alignment explanation
Indices: 60472--60532 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
60462 CCTTAAACAA
**
60472 TAAATAAAAGCATACATGTACACCTAAAATAG
1 TAAATAAAAGCATACACATACACCTAAAATAG
60504 TAAATAAAAGCATACACATACACCTAAAA
1 TAAATAAAAGCATACACATACACCTAAAA
60533 CATACTTTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.56, C:0.18, G:0.07, T:0.20
Consensus pattern (32 bp):
TAAATAAAAGCATACACATACACCTAAAATAG
Found at i:61393 original size:3 final size:3
Alignment explanation
Indices: 61375--61422 Score: 69
Period size: 3 Copynumber: 16.0 Consensus size: 3
61365 TTCATCGTTG
* * *
61375 TCA TCA TCG TCC TCA TCA TCA TCA TCA TCA TCA TCA TTA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
61423 CTCCCAACAA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.29, C:0.33, G:0.02, T:0.35
Consensus pattern (3 bp):
TCA
Found at i:63334 original size:14 final size:14
Alignment explanation
Indices: 63315--63345 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
63305 CAAAATTATT
63315 TAAATAAATTCAAA
1 TAAATAAATTCAAA
*
63329 TAAATAAATTCTAA
1 TAAATAAATTCAAA
63343 TAA
1 TAA
63346 TTTATATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.32
Consensus pattern (14 bp):
TAAATAAATTCAAA
Done.