Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007585.1 Hibiscus syriacus cultivar Beakdansim tig00021710_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: 55079
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.35
Found at i:13004 original size:43 final size:43
Alignment explanation
Indices: 12943--13159 Score: 371
Period size: 43 Copynumber: 5.0 Consensus size: 43
12933 ACCGTTACAA
*
12943 CAGGTCCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
1 CAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
12986 CAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
1 CAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
**
13029 CAGGTCCCTTTATTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
1 CAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
** *
13072 CATATCCCTTTGCTATGTGCAAGGGTAAGCCTTACAGTTTCCC
1 CAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
*
13115 CAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
1 CAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
13158 CA
1 CA
13160 AGCTCTTTTT
Statistics
Matches: 162, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 162 1.00
ACGTcount: A:0.18, C:0.27, G:0.24, T:0.32
Consensus pattern (43 bp):
CAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
Found at i:13174 original size:86 final size:86
Alignment explanation
Indices: 12943--13192 Score: 369
Period size: 86 Copynumber: 2.9 Consensus size: 86
12933 ACCGTTACAA
* *
12943 CAGGTCCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCCC-AGGTCCCTTTGCTGTGTGCA
1 CAGGTCCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAAGCT-CCTTTGCTATGTGCA
13007 AGGGTAAGCCTTACAGTTTCCC
65 AGGGTAAGCCTTACAGTTTCCC
* *
13029 CAGGTCCCTTTATTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCATATC-CCTTTGCTATGTGCA
1 CAGGTCCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCA-AGCTCCTTTGCTATGTGCA
13093 AGGGTAAGCCTTACAGTTTCCC
65 AGGGTAAGCCTTACAGTTTCCC
* * * * *
13115 CAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAAGCTCTTTTTCTATGTACAA
1 CAGGTCCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAAGCTCCTTTGCTATGTGCAA
*
13180 GGATAAGACCTTA
66 GGGTAAG-CCTTA
13193 TCATTTTTGC
Statistics
Matches: 148, Mismatches: 12, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
85 2 0.01
86 140 0.95
87 5 0.03
88 1 0.01
ACGTcount: A:0.20, C:0.26, G:0.22, T:0.32
Consensus pattern (86 bp):
CAGGTCCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAAGCTCCTTTGCTATGTGCAA
GGGTAAGCCTTACAGTTTCCC
Found at i:13181 original size:43 final size:43
Alignment explanation
Indices: 12949--13192 Score: 305
Period size: 43 Copynumber: 5.7 Consensus size: 43
12939 ACAACAGGTC
* *
12949 CCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCCC-AGGT
1 CCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAAGCT
*
12991 CCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCC-AGGT
1 -CCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAAGCT
** *
13034 CCCTTTATTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCATATC-
1 -CCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCA-AGCT
* * *
13078 CCTTTGCTATGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTT
1 CCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAAGCT
13121 CCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAAGCT
1 CCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAAGCT
* * * * *
13164 CTTTTTCTATGTACAAGGATAAGACCTTA
1 CCTTTGCTGTGTGCAAGGGTAAG-CCTTA
13193 TCATTTTTGC
Statistics
Matches: 178, Mismatches: 19, Indels: 7
0.87 0.09 0.03
Matches are distributed among these distances:
43 172 0.97
44 5 0.03
45 1 0.01
ACGTcount: A:0.20, C:0.25, G:0.22, T:0.33
Consensus pattern (43 bp):
CCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAAGCT
Found at i:13181 original size:129 final size:130
Alignment explanation
Indices: 12947--13192 Score: 388
Period size: 129 Copynumber: 1.9 Consensus size: 130
12937 TTACAACAGG
* *
12947 TCCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTCCCTTTGCTGTGTGCAAGGGT
1 TCCCTTTGCTATGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTCCCTTTGCTGTGTGCAAGGGT
* * * *
13012 AAGCCTTACAGTTTCCCCAGGTCCCTTTATTGTGTGCAAGGGTAAG-CCTTACAGTTTCCCCATA
66 AAGCCTTACAGTTTCCCCAAGTCCCTTTATTATGTACAAGGATAAGACCTTACAGTTTCCCCATA
*
13076 TCCCTTTGCTATGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTCCTTTGCTGTGTGCAAGGGT
1 TCCCTTTGCTATGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTCCCTTTGCTGTGTGCAAGGGT
* *
13141 AAGCCTTACAGTTTCCCCAAG-CTCTTTTTCTATGTACAAGGATAAGACCTTA
66 AAGCCTTACAGTTTCCCCAAGTCCCTTTAT-TATGTACAAGGATAAGACCTTA
13193 TCATTTTTGC
Statistics
Matches: 106, Mismatches: 9, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
128 6 0.06
129 95 0.90
130 5 0.05
ACGTcount: A:0.20, C:0.26, G:0.22, T:0.33
Consensus pattern (130 bp):
TCCCTTTGCTATGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTCCCTTTGCTGTGTGCAAGGGT
AAGCCTTACAGTTTCCCCAAGTCCCTTTATTATGTACAAGGATAAGACCTTACAGTTTCCCCATA
Found at i:17377 original size:2 final size:2
Alignment explanation
Indices: 17370--17400 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
17360 AAAAATATGT
17370 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
17401 CCAGGAAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19182 original size:64 final size:65
Alignment explanation
Indices: 19094--19246 Score: 184
Period size: 65 Copynumber: 2.4 Consensus size: 65
19084 TACACTAGGG
* * * * *
19094 GTGCATCGATACACTAATTACATTCAATGTTTC-AAAGAGCCAGGAGTGCATCGATGCATGG-TA
1 GTGCATCGGTACACAAAATGCATTCAATGTTTCAAAAGAGCCAAGAGTGCATCGATGCATGGCT-
19157 T
65 T
* * ** *
19158 GTGCATCGGTACACAAAATGCATTCGATGTTTCAAAATATTCAAGAGTGCATCGATGCTTGGCTT
1 GTGCATCGGTACACAAAATGCATTCAATGTTTCAAAAGAGCCAAGAGTGCATCGATGCATGGCTT
*
19223 GTGCCTCGGTACACAAAATGCATT
1 GTGCATCGGTACACAAAATGCATT
19247 AGAAATGGGT
Statistics
Matches: 76, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
64 28 0.37
65 47 0.62
66 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.29
Consensus pattern (65 bp):
GTGCATCGGTACACAAAATGCATTCAATGTTTCAAAAGAGCCAAGAGTGCATCGATGCATGGCTT
Found at i:20525 original size:23 final size:23
Alignment explanation
Indices: 20473--20525 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
20463 AATAAAAATA
* * *
20473 ATCCAAAACATCAATCCACAATC
1 ATCCAAAACATAAATCCAAAAAC
*
20496 ATCCAAAATATAAATCCAAAAAC
1 ATCCAAAACATAAATCCAAAAAC
*
20519 ATTCAAA
1 ATCCAAA
20526 TGTTTAACAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.55, C:0.26, G:0.00, T:0.19
Consensus pattern (23 bp):
ATCCAAAACATAAATCCAAAAAC
Found at i:22459 original size:23 final size:22
Alignment explanation
Indices: 22433--22500 Score: 59
Period size: 23 Copynumber: 3.0 Consensus size: 22
22423 AGTGCATTGA
22433 TGTACATTCAAGGAATGCATCGG
1 TGTACATTCAAGG-ATGCATCGG
* * *
22456 TGTATC-TTC-ATGATGTATCGA
1 TGTA-CATTCAAGGATGCATCGG
*
22477 TGCACATTCAAGGGATGCATCGG
1 TGTACATTCAA-GGATGCATCGG
22500 T
1 T
22501 ACACTGTCTA
Statistics
Matches: 34, Mismatches: 7, Indels: 8
0.69 0.14 0.16
Matches are distributed among these distances:
20 1 0.03
21 13 0.38
22 3 0.09
23 16 0.47
24 1 0.03
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (22 bp):
TGTACATTCAAGGATGCATCGG
Found at i:29192 original size:2 final size:2
Alignment explanation
Indices: 29185--29239 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
29175 CTTTTTAAAC
29185 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
29227 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
29240 CCCCCATCCC
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:29428 original size:24 final size:24
Alignment explanation
Indices: 29401--29493 Score: 96
Period size: 24 Copynumber: 3.9 Consensus size: 24
29391 ACGAAGATAT
* *
29401 CAGAAATCAAAACATAATTCAGAA
1 CAGAAATCAGAACAGAATTCAGAA
* * *
29425 CAGATATCAGAACAGAATCCAGAT
1 CAGAAATCAGAACAGAATTCAGAA
**
29449 CAGAAATCAGAACAGAATTCAGGT
1 CAGAAATCAGAACAGAATTCAGAA
***
29473 CATTTATCAGAACAGAATTCA
1 CAGAAATCAGAACAGAATTCA
29494 AGTCGGAAAT
Statistics
Matches: 58, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 58 1.00
ACGTcount: A:0.48, C:0.18, G:0.14, T:0.19
Consensus pattern (24 bp):
CAGAAATCAGAACAGAATTCAGAA
Found at i:29470 original size:12 final size:12
Alignment explanation
Indices: 29401--29470 Score: 70
Period size: 12 Copynumber: 5.8 Consensus size: 12
29391 ACGAAGATAT
* *
29401 CAGAAATCAAAA
1 CAGAATTCAGAA
*
29413 CATAATTCAGAA
1 CAGAATTCAGAA
29425 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
* *
29437 CAGAATCCAGAT
1 CAGAATTCAGAA
*
29449 CAGAAATCAGAA
1 CAGAATTCAGAA
29461 CAGAATTCAG
1 CAGAATTCAG
29471 GTCATTTATC
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
11 2 0.04
12 42 0.91
13 2 0.04
ACGTcount: A:0.51, C:0.19, G:0.14, T:0.16
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:29470 original size:48 final size:47
Alignment explanation
Indices: 29399--29507 Score: 128
Period size: 48 Copynumber: 2.3 Consensus size: 47
29389 AAACGAAGAT
* *
29399 ATCAGAAATCAAAACATAATTCAGAACAGATATCAGAACAGAATCCA
1 ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATCCA
** ** *
29446 GATCAGAAATCAGAACAGAATTCAGGTCATTTATCAGAACAGAATTCA
1 -ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATCCA
*
29494 AGTCGGAAATCAGA
1 A-TCAGAAATCAGA
29508 TAAAATATTT
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
47 1 0.02
48 51 0.98
ACGTcount: A:0.48, C:0.17, G:0.16, T:0.19
Consensus pattern (47 bp):
ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATCCA
Found at i:29505 original size:24 final size:24
Alignment explanation
Indices: 29400--29507 Score: 94
Period size: 24 Copynumber: 4.5 Consensus size: 24
29390 AACGAAGATA
* *
29400 TCAGAAATCAAAACATAATTC-AG
1 TCAGAAATCAGAACAGAATTCAAG
* * *
29423 AACAGATATCAGAACAGAA-TCCAG
1 -TCAGAAATCAGAACAGAATTCAAG
*
29447 ATCAGAAATCAGAACAGAATTCAGG
1 -TCAGAAATCAGAACAGAATTCAAG
***
29472 TCATTTATCAGAACAGAATTCAAG
1 TCAGAAATCAGAACAGAATTCAAG
*
29496 TCGGAAATCAGA
1 TCAGAAATCAGA
29508 TAAAATATTT
Statistics
Matches: 66, Mismatches: 16, Indels: 4
0.77 0.19 0.05
Matches are distributed among these distances:
23 2 0.03
24 61 0.92
25 3 0.05
ACGTcount: A:0.47, C:0.18, G:0.16, T:0.19
Consensus pattern (24 bp):
TCAGAAATCAGAACAGAATTCAAG
Found at i:31075 original size:31 final size:31
Alignment explanation
Indices: 31040--31139 Score: 77
Period size: 31 Copynumber: 3.2 Consensus size: 31
31030 TTAATTGCTT
31040 TCTTAAACACTCTCTGATCTTGAAACGGTTC
1 TCTTAAACACTCTCTGATCTTGAAACGGTTC
* *
31071 TCTTAACAGACT-TCTAGTATCCTTCACAAAC---TC
1 TCTTAA-ACACTCTCT-G-AT-CTT--GAAACGGTTC
31104 T-TCT-AACACTCTCTGATCTTGAAACGGTTC
1 TCT-TAAACACTCTCTGATCTTGAAACGGTTC
31134 TCTTAA
1 TCTTAA
31140 CAGACTTCTA
Statistics
Matches: 52, Mismatches: 4, Indels: 26
0.63 0.05 0.32
Matches are distributed among these distances:
27 4 0.08
29 3 0.06
30 6 0.12
31 16 0.31
32 10 0.19
33 6 0.12
34 3 0.06
36 4 0.08
ACGTcount: A:0.27, C:0.27, G:0.10, T:0.36
Consensus pattern (31 bp):
TCTTAAACACTCTCTGATCTTGAAACGGTTC
Found at i:31144 original size:63 final size:63
Alignment explanation
Indices: 31045--31167 Score: 246
Period size: 63 Copynumber: 2.0 Consensus size: 63
31035 TGCTTTCTTA
31045 AACACTCTCTGATCTTGAAACGGTTCTCTTAACAGACTTCTAGTATCCTTCACAAACTCTTCT
1 AACACTCTCTGATCTTGAAACGGTTCTCTTAACAGACTTCTAGTATCCTTCACAAACTCTTCT
31108 AACACTCTCTGATCTTGAAACGGTTCTCTTAACAGACTTCTAGTATCCTTCACAAACTCT
1 AACACTCTCTGATCTTGAAACGGTTCTCTTAACAGACTTCTAGTATCCTTCACAAACTCT
31168 CCTAGGATTA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 60 1.00
ACGTcount: A:0.28, C:0.28, G:0.10, T:0.34
Consensus pattern (63 bp):
AACACTCTCTGATCTTGAAACGGTTCTCTTAACAGACTTCTAGTATCCTTCACAAACTCTTCT
Found at i:32097 original size:7 final size:7
Alignment explanation
Indices: 32085--32116 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
32075 TGGTCAATTC
32085 CGGTCAA
1 CGGTCAA
32092 CGGTCAA
1 CGGTCAA
32099 CGGGTCAA
1 C-GGTCAA
32107 CGGTCAA
1 CGGTCAA
32114 CGG
1 CGG
32117 GTCGGGTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.25, C:0.28, G:0.34, T:0.12
Consensus pattern (7 bp):
CGGTCAA
Found at i:32106 original size:8 final size:8
Alignment explanation
Indices: 32086--32176 Score: 69
Period size: 8 Copynumber: 12.5 Consensus size: 8
32076 GGTCAATTCC
32086 GGTCAAC-
1 GGTCAACG
32093 GGTCAACG
1 GGTCAACG
32101 GGTCAAC-
1 GGTCAACG
32108 GGTCAACG
1 GGTCAACG
32116 GGT---CG
1 GGTCAACG
32121 GGTCAACG
1 GGTCAACG
32129 GGT---CG
1 GGTCAACG
32134 GGTCAACG
1 GGTCAACG
**
32142 GGTCGGGTCG
1 GGTC--AACG
32152 GGTCAACG
1 GGTCAACG
32160 GGT---CG
1 GGTCAACG
32165 GGTCAACG
1 GGTCAACG
32173 GGTC
1 GGTC
32177 GGGTCGGGTT
Statistics
Matches: 67, Mismatches: 4, Indels: 25
0.70 0.04 0.26
Matches are distributed among these distances:
5 15 0.22
7 14 0.21
8 32 0.48
10 6 0.09
ACGTcount: A:0.18, C:0.24, G:0.43, T:0.15
Consensus pattern (8 bp):
GGTCAACG
Found at i:32126 original size:13 final size:13
Alignment explanation
Indices: 32093--32181 Score: 106
Period size: 13 Copynumber: 6.3 Consensus size: 13
32083 TCCGGTCAAC
*
32093 GGTCAACGGGTCAAC
1 GGTCAACGGGTC--G
32108 GGTCAACGGGTCG
1 GGTCAACGGGTCG
32121 GGTCAACGGGTCG
1 GGTCAACGGGTCG
32134 GGTCAACGGGTCGGGTCG
1 GGTCAA-----CGGGTCG
32152 GGTCAACGGGTCG
1 GGTCAACGGGTCG
32165 GGTCAACGGGTCG
1 GGTCAACGGGTCG
32178 GGTC
1 GGTC
32182 GGGTTGTGAC
Statistics
Matches: 68, Mismatches: 1, Indels: 12
0.84 0.01 0.15
Matches are distributed among these distances:
13 43 0.63
15 12 0.18
18 13 0.19
ACGTcount: A:0.16, C:0.24, G:0.45, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:32152 original size:31 final size:31
Alignment explanation
Indices: 32114--32185 Score: 144
Period size: 31 Copynumber: 2.3 Consensus size: 31
32104 CAACGGTCAA
32114 CGGGTCGGGTCAACGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGTCGGGTCAACGGGT
32145 CGGGTCGGGTCAACGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGTCGGGTCAACGGGT
32176 CGGGTCGGGT
1 CGGGTCGGGT
32186 TGTGACCGGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.11, C:0.22, G:0.50, T:0.17
Consensus pattern (31 bp):
CGGGTCGGGTCAACGGGTCGGGTCAACGGGT
Found at i:32185 original size:18 final size:18
Alignment explanation
Indices: 32127--32168 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
32117 GTCGGGTCAA
32127 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
32145 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
32163 CGGGTC
1 CGGGTC
32169 AACGGGTCGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.10, C:0.24, G:0.50, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:32955 original size:2 final size:2
Alignment explanation
Indices: 32948--33007 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
32938 GGGGTGTTAC
32948 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
32990 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
33008 TATTTTTTCT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:34384 original size:2 final size:2
Alignment explanation
Indices: 34379--34413 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
34369 AAAAATCTTT
*
34379 TA TA TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
34414 TTCCAAGAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:35523 original size:24 final size:24
Alignment explanation
Indices: 35485--35566 Score: 94
Period size: 24 Copynumber: 3.4 Consensus size: 24
35475 AACAGAGATG
35485 TCAGAAATC-CAAACAGAATTCAGA
1 TCAGAAATCAC-AACAGAATTCAGA
* * * *
35509 TTAGATATCAGAACAGAATCCAGA
1 TCAGAAATCACAACAGAATTCAGA
*
35533 TCAGAAATCACAACAGAATTCAAA
1 TCAGAAATCACAACAGAATTCAGA
*
35557 TCGGAAATCA
1 TCAGAAATCA
35567 GATAAAACAT
Statistics
Matches: 47, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
24 47 1.00
ACGTcount: A:0.49, C:0.20, G:0.13, T:0.18
Consensus pattern (24 bp):
TCAGAAATCACAACAGAATTCAGA
Found at i:40229 original size:24 final size:24
Alignment explanation
Indices: 40202--40272 Score: 99
Period size: 24 Copynumber: 3.0 Consensus size: 24
40192 AAACGGAGAT
40202 ATCAGAAATCAAAACAGAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
*
40226 ATCA-AATATCAAAACAGAATCCAG
1 ATCAGAA-ATCAAAACAGAATTCAG
* *
40250 ATTAGAAATCAGAACAGAATTCA
1 ATCAGAAATCAAAACAGAATTCA
40273 AATAAAAATT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
23 2 0.05
24 37 0.90
25 2 0.05
ACGTcount: A:0.54, C:0.17, G:0.11, T:0.18
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:44489 original size:17 final size:17
Alignment explanation
Indices: 44467--44499 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
44457 ATAACTATTG
*
44467 AAAATAATAATATTTTT
1 AAAATAATAAAATTTTT
44484 AAAATAATAAAATTTT
1 AAAATAATAAAATTTT
44500 ATTGTTAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
AAAATAATAAAATTTTT
Found at i:44684 original size:31 final size:31
Alignment explanation
Indices: 44609--44684 Score: 86
Period size: 31 Copynumber: 2.5 Consensus size: 31
44599 GAAAATTCAT
* *
44609 TATATATTATTA-AA-ATAAAAGTATAATAT
1 TATATATTATTAGAATATAAAAGAATAATAA
* *
44638 TATATATCATTAGAATATTAAAGAATAA-AA
1 TATATATTATTAGAATATAAAAGAATAATAA
44668 TATCATATTATTAGAAT
1 TAT-ATATTATTAGAAT
44685 TATGAGTAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
29 11 0.28
30 6 0.15
31 22 0.56
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.39
Consensus pattern (31 bp):
TATATATTATTAGAATATAAAAGAATAATAA
Found at i:44723 original size:11 final size:11
Alignment explanation
Indices: 44707--44736 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
44697 TAATTTAATA
44707 ATTAAAATTTT
1 ATTAAAATTTT
44718 ATTAAAATTTT
1 ATTAAAATTTT
*
44729 AATAAAAT
1 ATTAAAAT
44737 AGTATAGTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
ATTAAAATTTT
Found at i:45095 original size:2 final size:2
Alignment explanation
Indices: 45083--45164 Score: 155
Period size: 2 Copynumber: 41.0 Consensus size: 2
45073 TTAATTCTTG
*
45083 AT AT AT TT 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
45125 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
45165 TTTTGGAAAA
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
2 78 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:49817 original size:43 final size:43
Alignment explanation
Indices: 49754--50045 Score: 388
Period size: 43 Copynumber: 6.8 Consensus size: 43
49744 CCGTTACAAT
* * * *
49754 AGGTCCCTTTGTTGTCTGCAAGGGTAGGCCTTATAGTTTCCCC
1 AGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCC
* * *
49797 AGGTCCTTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTTCCT
1 AGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCC
*
49840 AGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCTCC
1 AGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCC
* * *
49883 AGGTCCCTTTGTTGTGTGCAAGGGTAAGCTTTACAGTTTCCCT
1 AGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCC
* * *
49926 AGGTTCCTTTGATGTGTGCAAGGGTAAGCCTTACAGTTTCCCT
1 AGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCC
*
49969 AGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCC
1 AGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCC
* * * *
50012 AGG-CTCTTTTGATATGTGCAAGGATAAGACCTTA
1 AGGTC-CCTTTGCTGTGTGCAAGGGTAAG-CCTTA
50046 TCGTTTTTGC
Statistics
Matches: 222, Mismatches: 25, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
43 217 0.98
44 5 0.02
ACGTcount: A:0.18, C:0.22, G:0.25, T:0.35
Consensus pattern (43 bp):
AGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCC
Found at i:50939 original size:22 final size:22
Alignment explanation
Indices: 50887--50942 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
50877 CTCTTCAGAA
* *
50887 AAATGAAATATTTTGTAATTAT
1 AAATGAAATAATTTGCAATTAT
* *
50909 AAATAAAATAATTTGCATTTA-
1 AAATGAAATAATTTGCAATTAT
50930 ATAATGAAATAAT
1 A-AATGAAATAAT
50943 GAAATCATCA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
21 1 0.04
22 27 0.96
ACGTcount: A:0.52, C:0.02, G:0.07, T:0.39
Consensus pattern (22 bp):
AAATGAAATAATTTGCAATTAT
Found at i:51077 original size:2 final size:2
Alignment explanation
Indices: 51072--51100 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
51062 AAAAATATCT
51072 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
51101 TTCTAATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:54277 original size:23 final size:23
Alignment explanation
Indices: 54251--54318 Score: 56
Period size: 23 Copynumber: 3.2 Consensus size: 23
54241 GGGAAACTGT
54251 AAGGCTTACCTTTGCACACAGCA
1 AAGGCTTACCTTTGCACACAGCA
* * * * *
54274 AAGG--GACC--TGGAAACTG-T
1 AAGGCTTACCTTTGCACACAGCA
54292 AAGGCTTACCTTTGCACACAGCA
1 AAGGCTTACCTTTGCACACAGCA
54315 AAGG
1 AAGG
54319 GACCTGGGAA
Statistics
Matches: 30, Mismatches: 10, Indels: 10
0.60 0.20 0.20
Matches are distributed among these distances:
18 4 0.13
19 6 0.20
20 3 0.10
21 3 0.10
22 6 0.20
23 8 0.27
ACGTcount: A:0.32, C:0.25, G:0.24, T:0.19
Consensus pattern (23 bp):
AAGGCTTACCTTTGCACACAGCA
Found at i:54299 original size:41 final size:42
Alignment explanation
Indices: 54202--54366 Score: 296
Period size: 42 Copynumber: 4.0 Consensus size: 42
54192 GAGCCTAGGA
*
54202 AAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGG
1 AAACTGTAAGGCTTACCTTTGCACACAGCAAAGGGACCTGGG
54244 AAACTGTAAGGCTTACCTTTGCACACAGCAAAGGGACCT-GG
1 AAACTGTAAGGCTTACCTTTGCACACAGCAAAGGGACCTGGG
54285 AAACTGTAAGGCTTACCTTTGCACACAGCAAAGGGACCTGGG
1 AAACTGTAAGGCTTACCTTTGCACACAGCAAAGGGACCTGGG
* *
54327 AAACTATAAGGCTTACCTTTGCAGACAGCAAAGGGACCTG
1 AAACTGTAAGGCTTACCTTTGCACACAGCAAAGGGACCTG
54367 ATAATACTTC
Statistics
Matches: 119, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
41 41 0.34
42 78 0.66
ACGTcount: A:0.32, C:0.24, G:0.25, T:0.19
Consensus pattern (42 bp):
AAACTGTAAGGCTTACCTTTGCACACAGCAAAGGGACCTGGG
Found at i:54341 original size:83 final size:83
Alignment explanation
Indices: 54202--54366 Score: 303
Period size: 83 Copynumber: 2.0 Consensus size: 83
54192 GAGCCTAGGA
*
54202 AAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGAAACTGTAAGGCTTACCTTTGCA
1 AAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGAAACTATAAGGCTTACCTTTGCA
54267 CACAGCAAAGGGACCTGG
66 CACAGCAAAGGGACCTGG
*
54285 AAACTGTAAGGCTTACCTTTGCACACAGCAAAGGGACCTGGGAAACTATAAGGCTTACCTTTGCA
1 AAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGAAACTATAAGGCTTACCTTTGCA
*
54350 GACAGCAAAGGGACCTG
66 CACAGCAAAGGGACCTG
54367 ATAATACTTC
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
83 79 1.00
ACGTcount: A:0.32, C:0.24, G:0.25, T:0.19
Consensus pattern (83 bp):
AAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGAAACTATAAGGCTTACCTTTGCA
CACAGCAAAGGGACCTGG
Done.