Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005172.1 Hibiscus syriacus cultivar Beakdansim tig00011670_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: 64218
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:4151 original size:72 final size:73
Alignment explanation
Indices: 4065--4234 Score: 234
Period size: 83 Copynumber: 2.2 Consensus size: 73
4055 GTTTATTGAA
4065 AAACGCAGCAATAGAGTATAATA-TTGGCTAAAACGCCGTAATAGAGTGGTAAATTAGTGGCGTT
1 AAACGCAGCAATAGAGTATAATATTTGGCTAAAACGCCGTAATAGAGTGGTAAATTAGTGGCGTT
4129 TATACCAC
66 TATACCAC
4137 AAACGCAGCAATAGAGTATAATATTTGCGGCGTTTTGGCTAAAACGCCGTAATAGAGTGGTAAAT
1 AAACGCAGCAATAGAGTATAATA----------TTTGGCTAAAACGCCGTAATAGAGTGGTAAAT
4202 TAGTGGCGTTTATACCAC
56 TAGTGGCGTTTATACCAC
*
4220 AAACGCCGCAATAGA
1 AAACGCAGCAATAGA
4235 TTACACATAT
Statistics
Matches: 86, Mismatches: 1, Indels: 11
0.88 0.01 0.11
Matches are distributed among these distances:
72 23 0.27
83 63 0.73
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (73 bp):
AAACGCAGCAATAGAGTATAATATTTGGCTAAAACGCCGTAATAGAGTGGTAAATTAGTGGCGTT
TATACCAC
Found at i:4169 original size:42 final size:42
Alignment explanation
Indices: 4095--4234 Score: 151
Period size: 42 Copynumber: 3.4 Consensus size: 42
4085 ATATTGGCTA
* * *
4095 AAACGCCGTAATAGAGTGGTAAATTAGTGGCGTTTATACCAC
1 AAACGCCGCAATAGAGTGATAAATTAGCGGCGTTTATACCAC
* * * *
4137 AAACGCAGCAATAGAGT-ATAATATTTGCGGCGTTT-TGGCTA-
1 AAACGCCGCAATAGAGTGATAA-ATTAGCGGCGTTTAT-ACCAC
* * *
4178 AAACGCCGTAATAGAGTGGTAAATTAGTGGCGTTTATACCAC
1 AAACGCCGCAATAGAGTGATAAATTAGCGGCGTTTATACCAC
4220 AAACGCCGCAATAGA
1 AAACGCCGCAATAGA
4235 TTACACATAT
Statistics
Matches: 78, Mismatches: 15, Indels: 10
0.76 0.15 0.10
Matches are distributed among these distances:
41 32 0.41
42 46 0.59
ACGTcount: A:0.34, C:0.17, G:0.24, T:0.25
Consensus pattern (42 bp):
AAACGCCGCAATAGAGTGATAAATTAGCGGCGTTTATACCAC
Found at i:4194 original size:41 final size:41
Alignment explanation
Indices: 4088--4212 Score: 128
Period size: 41 Copynumber: 3.0 Consensus size: 41
4078 GAGTATAATA
* *
4088 TTGGCTAAAACGCCGTAATAGAGTGGTAAATTAGTGGCGTT
1 TTGGCTAAAACGCCGTAATAGAGTGATAAATTAGCGGCGTT
* * * * *
4129 TAT-ACCACAAACGCAGCAATAGAGT-ATAATATTTGCGGCGTT
1 T-TGGCTA-AAACGCCGTAATAGAGTGATAA-ATTAGCGGCGTT
* *
4171 TTGGCTAAAACGCCGTAATAGAGTGGTAAATTAGTGGCGTT
1 TTGGCTAAAACGCCGTAATAGAGTGATAAATTAGCGGCGTT
4212 T
1 T
4213 ATACCACAAA
Statistics
Matches: 65, Mismatches: 14, Indels: 10
0.73 0.16 0.11
Matches are distributed among these distances:
41 33 0.51
42 32 0.49
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.29
Consensus pattern (41 bp):
TTGGCTAAAACGCCGTAATAGAGTGATAAATTAGCGGCGTT
Found at i:4248 original size:42 final size:40
Alignment explanation
Indices: 4095--4254 Score: 121
Period size: 42 Copynumber: 3.8 Consensus size: 40
4085 ATATTGGCTA
*
4095 AAACGCCGTAATAGAGTGGTAAAT-TAGTGGCGTTTATACCAC
1 AAACGCCGCAATAGA-T--TAAATATAGTGGCGTTTATACCAC
* * * * * *
4137 AAACGCAGCAATAGAGTATAATATTTGCGGCGTTT-TGGCTA-
1 AAACGCCGCAATAGATTA-AATA-TAGTGGCGTTTAT-ACCAC
*
4178 AAACGCCGTAATAGAGTGGTAAAT-TAGTGGCGTTTATACCAC
1 AAACGCCGCAATAGA-T--TAAATATAGTGGCGTTTATACCAC
4220 AAACGCCGCAATAGATTACACATATAGTGGCGTTT
1 AAACGCCGCAATAGATTA-A-ATATAGTGGCGTTT
4255 TTTCCCTCAA
Statistics
Matches: 91, Mismatches: 15, Indels: 24
0.70 0.12 0.18
Matches are distributed among these distances:
39 4 0.04
40 4 0.04
41 28 0.31
42 50 0.55
43 3 0.03
44 2 0.02
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (40 bp):
AAACGCCGCAATAGATTAAATATAGTGGCGTTTATACCAC
Found at i:4252 original size:83 final size:83
Alignment explanation
Indices: 4088--4255 Score: 275
Period size: 83 Copynumber: 2.0 Consensus size: 83
4078 GAGTATAATA
4088 TTGGCTAAAACGCCGTAATAGAGTGGTAAATTAGTGGCGTTTATACCACAAACGCAGCAATAGAG
1 TTGGCTAAAACGCCGTAATAGAGTGGTAAATTAGTGGCGTTTATACCACAAACGCAGCAATAGAG
* *
4153 TATAATATTTGCGGCGTT
66 TACAATATTAGCGGCGTT
* *
4171 TTGGCTAAAACGCCGTAATAGAGTGGTAAATTAGTGGCGTTTATACCACAAACGCCGCAATAGAT
1 TTGGCTAAAACGCCGTAATAGAGTGGTAAATTAGTGGCGTTTATACCACAAACGCAGCAATAGAG
*
4236 TACACATA-TAGTGGCGTT
66 TACA-ATATTAGCGGCGTT
4254 TT
1 TT
4256 TTCCCTCAAA
Statistics
Matches: 79, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
83 76 0.96
84 3 0.04
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28
Consensus pattern (83 bp):
TTGGCTAAAACGCCGTAATAGAGTGGTAAATTAGTGGCGTTTATACCACAAACGCAGCAATAGAG
TACAATATTAGCGGCGTT
Found at i:4329 original size:41 final size:41
Alignment explanation
Indices: 4202--4462 Score: 239
Period size: 41 Copynumber: 6.3 Consensus size: 41
4192 AGTGGTAAAT
* *
4202 TAGTGGCGTTTATACCACAAACGCCGCAATAG-ATTACA-CATA
1 TAGTGGCGTTTTTA-GACAAACGCCGCAATAGTATTA-ATCA-A
*** * *
4244 TAGTGGCGTTTTTTCCCTCAAATGCCGTAATAGTGA-TAATCAA
1 TAGTGGCG-TTTTT-AGACAAACGCCGCAATAGT-ATTAATCAA
* *
4287 TAGTTGCGTTTTTAGACAAACGCCGCAATAGTATTACTCAA
1 TAGTGGCGTTTTTAGACAAACGCCGCAATAGTATTAATCAA
* *
4328 TAGTGGCATTTTTAGACAAAACACC-CAATAG-AGTTAATCAA
1 TAGTGGCGTTTTTAGAC-AAACGCCGCAATAGTA-TTAATCAA
* * *
4369 TACTGGCGTTTTTAGACAAACGCCACAATAGTGTTAATCAA
1 TAGTGGCGTTTTTAGACAAACGCCGCAATAGTATTAATCAA
* * *
4410 TAGTGGCGTTTTTTA-ACAAACTCCACAATAGT-GTAATCAA
1 TAGTGGCG-TTTTTAGACAAACGCCGCAATAGTATTAATCAA
4450 TAGTGGCGTTTTT
1 TAGTGGCGTTTTT
4463 TGTATAAATG
Statistics
Matches: 185, Mismatches: 23, Indels: 25
0.79 0.10 0.11
Matches are distributed among these distances:
39 5 0.03
40 23 0.12
41 100 0.54
42 25 0.14
43 27 0.15
44 4 0.02
45 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (41 bp):
TAGTGGCGTTTTTAGACAAACGCCGCAATAGTATTAATCAA
Found at i:4463 original size:41 final size:41
Alignment explanation
Indices: 4272--4462 Score: 253
Period size: 41 Copynumber: 4.7 Consensus size: 41
4262 CAAATGCCGT
* * *
4272 AATAGTGATAATCAATAGTTGCGTTTTTAGACAAACGCCGC
1 AATAGTGTTAATCAATAGTGGCGTTTTTAGACAAACGCCAC
* * * *
4313 AATAGTATTACTCAATAGTGGCATTTTTAGACAAAACACC-C
1 AATAGTGTTAATCAATAGTGGCGTTTTTAGAC-AAACGCCAC
* *
4354 AATAGAGTTAATCAATACTGGCGTTTTTAGACAAACGCCAC
1 AATAGTGTTAATCAATAGTGGCGTTTTTAGACAAACGCCAC
*
4395 AATAGTGTTAATCAATAGTGGCGTTTTTTA-ACAAACTCCAC
1 AATAGTGTTAATCAATAGTGGCG-TTTTTAGACAAACGCCAC
4436 AATAGTG-TAATCAATAGTGGCGTTTTT
1 AATAGTGTTAATCAATAGTGGCGTTTTT
4463 TGTATAAATG
Statistics
Matches: 132, Mismatches: 15, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
39 5 0.04
40 21 0.16
41 94 0.71
42 12 0.09
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (41 bp):
AATAGTGTTAATCAATAGTGGCGTTTTTAGACAAACGCCAC
Found at i:5771 original size:42 final size:43
Alignment explanation
Indices: 5712--5810 Score: 146
Period size: 42 Copynumber: 2.3 Consensus size: 43
5702 CTTTTTTTTA
5712 CAAACGCCGCAATAGGTACAATATTTAGTGG-CATTTTCGCAC
1 CAAACGCCGCAATAGGTACAATATTTAGTGGTCATTTTCGCAC
* ** *
5754 CAAACGCCGCAATAGGTATAATATTTAGTGGTGTTTTTTGCAC
1 CAAACGCCGCAATAGGTACAATATTTAGTGGTCATTTTCGCAC
*
5797 CAAACGCCGTAATA
1 CAAACGCCGCAATA
5811 TTTGGGGATA
Statistics
Matches: 51, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
42 30 0.59
43 21 0.41
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.28
Consensus pattern (43 bp):
CAAACGCCGCAATAGGTACAATATTTAGTGGTCATTTTCGCAC
Found at i:5968 original size:42 final size:41
Alignment explanation
Indices: 5828--5968 Score: 140
Period size: 41 Copynumber: 3.4 Consensus size: 41
5818 ATATACCGGG
* * ** * * *
5828 GTTTTTATATAAACGCCACAAAATAGTACTACTTTAGCGGC
1 GTTTTTATAAAAACGCCGCAAAATAGTAAAATTTTAGTGAC
* *
5869 GTTTATATAAAAACGCCGCAAAATAGTAAAATTTTAGTGGC
1 GTTTTTATAAAAACGCCGCAAAATAGTAAAATTTTAGTGAC
* * *
5910 GTTTTTAAAAAAACGCCGTAAAATAATTAGAAATTTT-GTGAC
1 GTTTTTATAAAAACGCCGCAAAAT-AGTA-AAATTTTAGTGAC
*
5952 GTTTTTATATAAACGCC
1 GTTTTTATAAAAACGCC
5969 CCAATACAAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
41 55 0.65
42 22 0.26
43 7 0.08
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.33
Consensus pattern (41 bp):
GTTTTTATAAAAACGCCGCAAAATAGTAAAATTTTAGTGAC
Found at i:6591 original size:23 final size:23
Alignment explanation
Indices: 6561--6612 Score: 95
Period size: 23 Copynumber: 2.3 Consensus size: 23
6551 TTGAGAGGAA
*
6561 ATGAAGCTTAAAAACTGAATGAG
1 ATGAAGCTTAAAAACTAAATGAG
6584 ATGAAGCTTAAAAACTAAATGAG
1 ATGAAGCTTAAAAACTAAATGAG
6607 ATGAAG
1 ATGAAG
6613 TTCAATAACA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.50, C:0.08, G:0.21, T:0.21
Consensus pattern (23 bp):
ATGAAGCTTAAAAACTAAATGAG
Found at i:6610 original size:28 final size:24
Alignment explanation
Indices: 6552--6612 Score: 72
Period size: 23 Copynumber: 2.6 Consensus size: 24
6542 GATTTTATTT
*
6552 TGAGAGGAAATGAAGCTTAAAAAC
1 TGAGATGAAATGAAGCTTAAAAAC
*
6576 TGA-ATGAGATGAAGCTTAAAAAC
1 TGAGATGAAATGAAGCTTAAAAAC
* *
6599 T-AAATGAGATGAAG
1 TGAGATGAAATGAAG
6613 TTCAATAACA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
22 1 0.03
23 30 0.88
24 3 0.09
ACGTcount: A:0.49, C:0.07, G:0.25, T:0.20
Consensus pattern (24 bp):
TGAGATGAAATGAAGCTTAAAAAC
Found at i:7993 original size:12 final size:12
Alignment explanation
Indices: 7976--8009 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
7966 ACTGATTGGG
7976 AGAAGATGAAAA
1 AGAAGATGAAAA
7988 AGAAGATGAAAA
1 AGAAGATGAAAA
8000 AGAAGATGAA
1 AGAAGATGAA
8010 GGGTCACTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.65, C:0.00, G:0.26, T:0.09
Consensus pattern (12 bp):
AGAAGATGAAAA
Found at i:19219 original size:21 final size:21
Alignment explanation
Indices: 19195--19246 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
19185 TGAAGTAAGG
19195 GAAGCAGAGAGAGCAACAGCA
1 GAAGCAGAGAGAGCAACAGCA
** **
19216 GAAGCAGCTAGAGCAGTAGCA
1 GAAGCAGAGAGAGCAACAGCA
19237 GAAGCAGAGA
1 GAAGCAGAGA
19247 AATAAGCAAC
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.44, C:0.17, G:0.35, T:0.04
Consensus pattern (21 bp):
GAAGCAGAGAGAGCAACAGCA
Found at i:19263 original size:21 final size:21
Alignment explanation
Indices: 19241--19319 Score: 77
Period size: 21 Copynumber: 3.7 Consensus size: 21
19231 GTAGCAGAAG
19241 CAGAGAAATAAGCAACGGCAGCA
1 CAGAG-AA-AAGCAACGGCAGCA
** *
19264 CAGAGAAAAGCAACGATAACA
1 CAGAGAAAAGCAACGGCAGCA
* *
19285 CAGAGAGAAGCAACGGCAACA
1 CAGAGAAAAGCAACGGCAGCA
* *
19306 TAGAGAGAAGCAAC
1 CAGAGAAAAGCAAC
19320 ATATCAGCAG
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
21 42 0.86
22 2 0.04
23 5 0.10
ACGTcount: A:0.51, C:0.20, G:0.25, T:0.04
Consensus pattern (21 bp):
CAGAGAAAAGCAACGGCAGCA
Found at i:19297 original size:42 final size:42
Alignment explanation
Indices: 19250--19332 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 42
19240 GCAGAGAAAT
*
19250 AAGCAACGGCAGCACAGAGAAAAGCAACGATAACA-CAGAGAG
1 AAGCAACGGCAACACAGAGAAAAGCAAC-ATAACAGCAGAGAG
* * *
19292 AAGCAACGGCAACATAGAGAGAAGCAACATATCAGCAGAGA
1 AAGCAACGGCAACACAGAGAAAAGCAACATAACAGCAGAGA
19333 TGTGAAGAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
41 5 0.14
42 31 0.86
ACGTcount: A:0.49, C:0.20, G:0.25, T:0.05
Consensus pattern (42 bp):
AAGCAACGGCAACACAGAGAAAAGCAACATAACAGCAGAGAG
Found at i:19331 original size:21 final size:21
Alignment explanation
Indices: 19262--19332 Score: 81
Period size: 21 Copynumber: 3.4 Consensus size: 21
19252 GCAACGGCAG
*
19262 CACAGAGAAAAGCAACGATAA
1 CACAGAGAGAAGCAACGATAA
**
19283 CACAGAGAGAAGCAACGGCAA
1 CACAGAGAGAAGCAACGATAA
* *
19304 CATAGAGAGAAGCAAC-ATAT
1 CACAGAGAGAAGCAACGATAA
19324 CAGCAGAGA
1 CA-CAGAGA
19333 TGTGAAGAAT
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 3 0.07
21 38 0.93
ACGTcount: A:0.51, C:0.20, G:0.24, T:0.06
Consensus pattern (21 bp):
CACAGAGAGAAGCAACGATAA
Found at i:19712 original size:44 final size:44
Alignment explanation
Indices: 19655--19751 Score: 158
Period size: 44 Copynumber: 2.2 Consensus size: 44
19645 TTTGTAAAAA
* * *
19655 AAACGCTGCAATATACCATACATTTAGTGGCGTTTGTATACTAG
1 AAACGCCGCAATATACCATACATTTAGCGGCATTTGTATACTAG
*
19699 AAACGCCGCAATATACCATACATTTAGCGGCATTTTTATACTAG
1 AAACGCCGCAATATACCATACATTTAGCGGCATTTGTATACTAG
19743 AAACGCCGC
1 AAACGCCGC
19752 TAATTCTCAA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 49 1.00
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.28
Consensus pattern (44 bp):
AAACGCCGCAATATACCATACATTTAGCGGCATTTGTATACTAG
Found at i:19948 original size:42 final size:42
Alignment explanation
Indices: 19865--19985 Score: 118
Period size: 42 Copynumber: 2.8 Consensus size: 42
19855 TACGGTATTC
* *
19865 GTAAGTAAAACACCGCTAAATC-TCAACACCTACTGCAGCGTTT
1 GTAAG-AAAACGCCGCTAAA-CATCAACACCTATTGCAGCGTTT
* **
19908 GTAAGAAAACGCTGCTAAACATCAACACCTATTGTGGCGTTT
1 GTAAGAAAACGCCGCTAAACATCAACACCTATTGCAGCGTTT
* ** * *
19950 TTCTGACAAACGCCGCTAAATAACAACACCTATTGC
1 GTAAGA-AAACGCCGCTAAACATCAACACCTATTGC
19986 GATGTTTTAA
Statistics
Matches: 64, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
41 1 0.02
42 33 0.52
43 30 0.47
ACGTcount: A:0.35, C:0.26, G:0.15, T:0.24
Consensus pattern (42 bp):
GTAAGAAAACGCCGCTAAACATCAACACCTATTGCAGCGTTT
Found at i:20375 original size:77 final size:77
Alignment explanation
Indices: 20256--20410 Score: 310
Period size: 77 Copynumber: 2.0 Consensus size: 77
20246 CACCCGACTT
20256 TTCATATGTTTCAAACTCGTTCTTTTTCGTTAAAAATTAACAACAATTTGAGTTGGACATTAACC
1 TTCATATGTTTCAAACTCGTTCTTTTTCGTTAAAAATTAACAACAATTTGAGTTGGACATTAACC
20321 TACCGACTGAGA
66 TACCGACTGAGA
20333 TTCATATGTTTCAAACTCGTTCTTTTTCGTTAAAAATTAACAACAATTTGAGTTGGACATTAACC
1 TTCATATGTTTCAAACTCGTTCTTTTTCGTTAAAAATTAACAACAATTTGAGTTGGACATTAACC
20398 TACCGACTGAGA
66 TACCGACTGAGA
20410 T
1 T
20411 ATGATAAAAT
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
77 78 1.00
ACGTcount: A:0.32, C:0.18, G:0.13, T:0.37
Consensus pattern (77 bp):
TTCATATGTTTCAAACTCGTTCTTTTTCGTTAAAAATTAACAACAATTTGAGTTGGACATTAACC
TACCGACTGAGA
Found at i:26683 original size:54 final size:54
Alignment explanation
Indices: 26601--26705 Score: 147
Period size: 54 Copynumber: 1.9 Consensus size: 54
26591 CATTGCCTCC
* * *
26601 ATAAGAAGTGGTGCTTGGTCTCGGTTCAAAATCACTAGTGAATGATTTCTTACA
1 ATAAGAAGTGATGCTCGGTCTAGGTTCAAAATCACTAGTGAATGATTTCTTACA
* * * *
26655 ATAAGATGTGATGCTCGGTCTAGGTTCAAATTCACTAGTTAATGTTTTCTT
1 ATAAGAAGTGATGCTCGGTCTAGGTTCAAAATCACTAGTGAATGATTTCTT
26706 CACTCCTTTA
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
54 44 1.00
ACGTcount: A:0.28, C:0.14, G:0.21, T:0.37
Consensus pattern (54 bp):
ATAAGAAGTGATGCTCGGTCTAGGTTCAAAATCACTAGTGAATGATTTCTTACA
Found at i:26706 original size:135 final size:134
Alignment explanation
Indices: 26463--26954 Score: 585
Period size: 135 Copynumber: 3.6 Consensus size: 134
26453 ATTATTTCTT
* * * ** **
26463 ACCATAAGAAGTGATG-TTCGGTATGGGTTCAAAATCACCGGTGAATGATTTCTGGCCATAAGAA
1 ACCATAAGAAGTGGTGCTT-GGTCTCGGTTCAAAATCACTAGTGAATGATTTCTTACCATAAGAA
* * * * * *
26527 GTGGTGCTCAGTCTCA-GTTCAAAATCGCTAGGAAAAGTTTTCTTCACTCCTTTAAGATCAACAT
65 GTGATGCTCGGTCT-AGGTTCAAATTCACTA-GTAATGTTTTCTTCACTCCTTTAAGATCAACAT
26591 CATTGCC
128 CATTGCC
* * *
26598 TCCATAAGAAGTGGTGCTTGGTCTCGGTTCAAAATCACTAGTGAATGATTTCTTACAATAAGATG
1 ACCATAAGAAGTGGTGCTTGGTCTCGGTTCAAAATCACTAGTGAATGATTTCTTACCATAAGAAG
26663 TGATGCTCGGTCTAGGTTCAAATTCACTAGTTAATGTTTTCTTCACTCCTTTAAGATCAACATCA
66 TGATGCTCGGTCTAGGTTCAAATTCACTAG-TAATGTTTTCTTCACTCCTTTAAGATCAACATCA
26728 TTGCC
130 TTGCC
* * * * *
26733 ACCATAAGAAGTGGTGCTTGGTCTCTGCTCAAAATCAATAGTGAATGATTTCTAACCATAAGACG
1 ACCATAAGAAGTGGTGCTTGGTCTCGGTTCAAAATCACTAGTGAATGATTTCTTACCATAAGAAG
* * *
26798 TGATGTTCGGTCTCGGTTCAAATTCACTAGTAATTGATTTCTTCACTCCTTTAAGATCAACATCA
66 TGATGCTCGGTCTAGGTTCAAATTCACTAGTAA-TGTTTTCTTCACTCCTTTAAGATCAACATCA
*
26863 TTGTC
130 TTGCC
* ** * * * * * *
26868 GCCATAAGCTGTGGTACTCGATTTCTGTTCAAAATCACTAGTGAATGATTT-ATAGCCATAAGAA
1 ACCATAAGAAGTGGTGCTTGGTCTCGGTTCAAAATCACTAGTGAATGATTTCTTA-CCATAAGAA
* *
26932 GTGGTGCTCGGTCTCGGTTCAAA
65 GTGATGCTCGGTCTAGGTTCAAA
26955 ATAGCTCTCC
Statistics
Matches: 311, Mismatches: 41, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
134 6 0.02
135 303 0.97
136 2 0.01
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (134 bp):
ACCATAAGAAGTGGTGCTTGGTCTCGGTTCAAAATCACTAGTGAATGATTTCTTACCATAAGAAG
TGATGCTCGGTCTAGGTTCAAATTCACTAGTAATGTTTTCTTCACTCCTTTAAGATCAACATCAT
TGCC
Found at i:26819 original size:54 final size:54
Alignment explanation
Indices: 26733--26839 Score: 128
Period size: 54 Copynumber: 2.0 Consensus size: 54
26723 CATCATTGCC
* *
26733 ACCATAAGAAGTGGTGCTTGGTCTCTGCTCAAAATCAATAGTGAA-TGATTTCTA
1 ACCATAAGAAGTGATGCTTGGTCTCGGCTCAAAATCAATAGT-AATTGATTTCTA
* * * *
26787 ACCATAAGACGTGATG-TTCGGTCTCGGTTCAAATTCACTAGTAATTGATTTCT
1 ACCATAAGAAGTGATGCTT-GGTCTCGGCTCAAAATCAATAGTAATTGATTTCT
26840 TCACTCCTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
53 4 0.09
54 41 0.91
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.34
Consensus pattern (54 bp):
ACCATAAGAAGTGATGCTTGGTCTCGGCTCAAAATCAATAGTAATTGATTTCTA
Found at i:32752 original size:25 final size:24
Alignment explanation
Indices: 32710--32766 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
32700 GTTTAAAAAT
32710 AAAACTTAAAATAAAAATGAAAACA
1 AAAACTTAAAATAAAAAT-AAAACA
* *
32735 AAAACTTGAAAA-GAAAATAAAAGA
1 AAAACTT-AAAATAAAAATAAAACA
32759 AATAACTT
1 AA-AACTT
32767 TATAAAATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 7 0.25
25 17 0.61
26 4 0.14
ACGTcount: A:0.68, C:0.07, G:0.07, T:0.18
Consensus pattern (24 bp):
AAAACTTAAAATAAAAATAAAACA
Found at i:39493 original size:17 final size:18
Alignment explanation
Indices: 39473--39513 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
39463 AGGGATTTGG
*
39473 TAAAAAGGA-TTAAATAA
1 TAAAAAGGATTTAAAGAA
*
39490 TAAAAATGATTTAAAGAA
1 TAAAAAGGATTTAAAGAA
39508 -AAAAAG
1 TAAAAAG
39514 AAAATAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.66, C:0.00, G:0.12, T:0.22
Consensus pattern (18 bp):
TAAAAAGGATTTAAAGAA
Found at i:40115 original size:18 final size:17
Alignment explanation
Indices: 40094--40143 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 17
40084 TTTAAAAATA
40094 AAAATGAAAACGAAAACG
1 AAAATGAAAACGAAAA-G
*
40112 AAAACGAAAACTTGAAAAG
1 AAAATGAAAAC--GAAAAG
40131 AAAAT-AAAA-GAAA
1 AAAATGAAAACGAAA
40144 TAACTTTATA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
15 4 0.14
18 14 0.50
19 5 0.18
20 5 0.18
ACGTcount: A:0.70, C:0.08, G:0.14, T:0.08
Consensus pattern (17 bp):
AAAATGAAAACGAAAAG
Found at i:42729 original size:45 final size:45
Alignment explanation
Indices: 42648--43240 Score: 511
Period size: 45 Copynumber: 13.2 Consensus size: 45
42638 TTCCGCGATT
* * * *
42648 AAGTCAA-AATAAC-ACAATAAAAGGTTGACTAT-TCTTCATGAGA
1 AAGTCAAGAATGACAACACTAAAAGATTGACT-TCTCTTCACGAGA
* * * *
42691 AAGTCAAGAAGGATAACATTAAAAGATCGACTTCTCTTCACGAG-
1 AAGTCAAGAATGACAACACTAAAAGATTGACTTCTCTTCACGAGA
* * * * ***
42735 AATTCAAGAATGACAACAATAAAAGATTAACTTTTCTTTGTGAGA
1 AAGTCAAGAATGACAACACTAAAAGATTGACTTCTCTTCACGAGA
* * * * *
42780 AAGTCAAGAATAACATCACTAAAAGGTTGACTTATCTTCATGAGA
1 AAGTCAAGAATGACAACACTAAAAGATTGACTTCTCTTCACGAGA
* * * *
42825 AAGTTAAGTAGGACAATACTAAAAGATTGA-TTCCTCTTCACGAGA
1 AAGTCAAGAATGACAACACTAAAAGATTGACTT-CTCTTCACGAGA
* * * * * *
42870 AAGTCAAGAAGGACAACACT-AATGATTGACTCCTTTTAACAAGA
1 AAGTCAAGAATGACAACACTAAAAGATTGACTTCTCTTCACGAGA
* * * * *
42914 AAGTTAAGGAA-GATAACACTGAAAGATTGACTTCTCTTCATGATA
1 AAGTCAA-GAATGACAACACTAAAAGATTGACTTCTCTTCACGAGA
* * * * **
42959 AAGTCAAGAATAACATCACTAAAAGGTTGACTTCTCCTCATAAGA
1 AAGTCAAGAATGACAACACTAAAAGATTGACTTCTCTTCACGAGA
* * * * * * *
43004 AAGTGAAGTAGGACAATATTAAAAGATTGACTCCTCTTCATGAGA
1 AAGTCAAGAATGACAACACTAAAAGATTGACTTCTCTTCACGAGA
* * * *
43049 AAGTCAAGAATGACAACACTAAAATATTGAATCCTTTTCACGAGA
1 AAGTCAAGAATGACAACACTAAAAGATTGACTTCTCTTCACGAGA
* *
43094 AAGTCAAGGAA-GACAACATTGAAAGATTGACTTCTCTTCACGAGAA
1 AAGTCAA-GAATGACAACACTAAAAGATTGACTTCTCTTCACGAG-A
* * * **
43140 AAGTCAAGAATGATAATACTAAATGATCAAC-TCTGCTTCACGAGA
1 AAGTCAAGAATGACAACACTAAAAGATTGACTTCT-CTTCACGAGA
* * *
43185 AAGTTAAGAATTACAATACTAAAAGATTGACTTCTCTTCACGAGA
1 AAGTCAAGAATGACAACACTAAAAGATTGACTTCTCTTCACGAGA
43230 AAGTCAAGAAT
1 AAGTCAAGAAT
43241 AACATTAAAT
Statistics
Matches: 435, Mismatches: 101, Indels: 26
0.77 0.18 0.05
Matches are distributed among these distances:
43 7 0.02
44 74 0.17
45 318 0.73
46 36 0.08
ACGTcount: A:0.42, C:0.16, G:0.16, T:0.26
Consensus pattern (45 bp):
AAGTCAAGAATGACAACACTAAAAGATTGACTTCTCTTCACGAGA
Found at i:42987 original size:179 final size:178
Alignment explanation
Indices: 42680--43239 Score: 601
Period size: 179 Copynumber: 3.1 Consensus size: 178
42670 GGTTGACTAT
* * * * * * * * * * *
42680 TCTTCATGAGAAAGTCAAGAAGGATAACATTAAAAGATCGACTTCTCTTCACGAG-AATTCAA-G
1 TCTTCACGAGAAAGTCAAGAAGGACAACACT-AAATATTGAATCCTTTTAACAAGAAAGTCAAGG
* * * * ** *
42743 AATGACAACAATAAAAGATTAACTTTTCTTTGTGAGAAAGTCAAGAATAACATCACTAAAAGGTT
65 AA-GACAACACTGAAAGATTGACTTCTCTTCATGAAAAAGTCAAGAATAACATCACTAAAAGGTT
42808 GACTTATCTTCATGAGAAAGTTAAGTAGGACAATACTAAAAGATTGATTCC
129 GACTT-TCTTCATGAGAAAGTTAAGTAGGACAATACTAAAAGATTGATTCC
* *
42859 TCTTCACGAGAAAGTCAAGAAGGACAACACT-AATGATTGACTCCTTTTAACAAGAAAGTTAAGG
1 TCTTCACGAGAAAGTCAAGAAGGACAACACTAAAT-ATTGAATCCTTTTAACAAGAAAGTCAAGG
* *
42923 AAGATAACACTGAAAGATTGACTTCTCTTCATGATAAAGTCAAGAATAACATCACTAAAAGGTTG
65 AAGACAACACTGAAAGATTGACTTCTCTTCATGAAAAAGTCAAGAATAACATCACTAAAAGGTTG
* * * * *
42988 ACTTCTCCTCATAAGAAAGTGAAGTAGGACAATATTAAAAGATTGACTCC
130 ACTT-TCTTCATGAGAAAGTTAAGTAGGACAATACTAAAAGATTGATTCC
* * * *
43038 TCTTCATGAGAAAGTCAAGAATGACAACACTAAAATATTGAATCCTTTTCACGAGAAAGTCAAGG
1 TCTTCACGAGAAAGTCAAGAAGGACAACACT-AAATATTGAATCCTTTTAACAAGAAAGTCAAGG
* * * *
43103 AAGACAACATTGAAAGATTGACTTCTCTTCACGAGAAAAGTCAAGAATGATA-AT-ACTAAATGA
65 AAGACAACACTGAAAGATTGACTTCTCTTCATGA-AAAAGTCAAGAAT-A-ACATCACTAAAAGG
** * * * **
43166 TCAACTCTGCTTCACGAGAAAGTTAAGAATTACAATACTAAAAGATTGACTT-C
127 TTGACT-TTCTTCATGAGAAAGTTAAGTAGGACAATACTAAAAGATTGA-TTCC
43219 TCTTCACGAGAAAGTCAAGAA
1 TCTTCACGAGAAAGTCAAGAA
43240 TAACATTAAA
Statistics
Matches: 321, Mismatches: 50, Indels: 18
0.83 0.13 0.05
Matches are distributed among these distances:
177 2 0.01
178 14 0.04
179 161 0.50
180 59 0.18
181 79 0.25
182 5 0.02
183 1 0.00
ACGTcount: A:0.42, C:0.16, G:0.16, T:0.26
Consensus pattern (178 bp):
TCTTCACGAGAAAGTCAAGAAGGACAACACTAAATATTGAATCCTTTTAACAAGAAAGTCAAGGA
AGACAACACTGAAAGATTGACTTCTCTTCATGAAAAAGTCAAGAATAACATCACTAAAAGGTTGA
CTTTCTTCATGAGAAAGTTAAGTAGGACAATACTAAAAGATTGATTCC
Found at i:49694 original size:23 final size:23
Alignment explanation
Indices: 49668--49712 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
49658 CAAATTCAAA
* *
49668 TTAGGATTTATATTTTTTATTTT
1 TTAGGAATTATATTTTTAATTTT
*
49691 TTAGGAATTATCTTTTTAATTT
1 TTAGGAATTATATTTTTAATTT
49713 GAATGTTATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.24, C:0.02, G:0.09, T:0.64
Consensus pattern (23 bp):
TTAGGAATTATATTTTTAATTTT
Found at i:63491 original size:45 final size:46
Alignment explanation
Indices: 63442--63610 Score: 222
Period size: 45 Copynumber: 3.8 Consensus size: 46
63432 GATAAAACCT
*
63442 CTTACCATTT-ATCCCATAAGCTTGTAAGCTTATTTTACCAATATA
1 CTTACCATTTAATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
* * *
63487 CTTACTATTTAATACCATAAGCTTGTAAGCTTA-TTTACCAATATA
1 CTTACCATTTAATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
* * **
63532 CTTATCATTTAATCCCATAAGCTCATAAGCTTATTTTA-GTA-ATA
1 CTTACCATTTAATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
*
63576 CTTACCATTTAATCCCATAA-ATCGTAAGCTTATTT
1 CTTACCATTTAATCCCATAAGCTCGTAAGCTTATTT
63611 GCCAGTTTAT
Statistics
Matches: 110, Mismatches: 12, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
43 13 0.12
44 22 0.20
45 50 0.45
46 25 0.23
ACGTcount: A:0.33, C:0.20, G:0.07, T:0.40
Consensus pattern (46 bp):
CTTACCATTTAATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
Done.