Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006193.1 Hibiscus syriacus cultivar Beakdansim tig00014737_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: 63120
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:4012 original size:34 final size:34
Alignment explanation
Indices: 3957--4045 Score: 83
Period size: 34 Copynumber: 2.6 Consensus size: 34
3947 TAGTGTAACC
* *
3957 AATGAACTAGATGCA-TGAATGAAGTAGCTT-ACTA
1 AATGAACTAAATG-ATTAAATGAAGTA-CTTCACTA
* * *
3991 AATGATCTAAATGATTAAATGAATTACTTCCCTA
1 AATGAACTAAATGATTAAATGAAGTACTTCACTA
* *
4025 AATGAACTAGATGCTTAAATG
1 AATGAACTAAATGATTAAATG
4046 TAATGCATTC
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
33 4 0.09
34 41 0.91
ACGTcount: A:0.42, C:0.12, G:0.16, T:0.30
Consensus pattern (34 bp):
AATGAACTAAATGATTAAATGAAGTACTTCACTA
Found at i:10073 original size:18 final size:18
Alignment explanation
Indices: 10047--10086 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
10037 CTTTAGATTA
* *
10047 TTTATTTAATTATTTTCT
1 TTTAATTAATTATTATCT
*
10065 TTTAATTAATTCTTATCT
1 TTTAATTAATTATTATCT
10083 TTTA
1 TTTA
10087 TTTTTAAAAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.25, C:0.07, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTAATTAATTATTATCT
Found at i:10231 original size:31 final size:30
Alignment explanation
Indices: 10168--10255 Score: 95
Period size: 31 Copynumber: 2.8 Consensus size: 30
10158 CCCTTTTTTA
* **
10168 TTTTATTTTGTTTTATCTTTTATTTTCCCACT
1 TTTTATTTT-TTTTAT-TTTTCTTTTAACACT
10200 TTTTATTTTTTTTATTTTCTCTTTTAACACT
1 TTTTATTTTTTTTATTTT-TCTTTTAACACT
* *
10231 TTTTATATATTATTATTTTTCTTTT
1 TTTTAT-TTTTTTTATTTTTCTTTT
10256 CTGAAATTTA
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
30 3 0.06
31 27 0.55
32 19 0.39
ACGTcount: A:0.16, C:0.11, G:0.01, T:0.72
Consensus pattern (30 bp):
TTTTATTTTTTTTATTTTTCTTTTAACACT
Found at i:15666 original size:86 final size:86
Alignment explanation
Indices: 15483--15657 Score: 305
Period size: 86 Copynumber: 2.0 Consensus size: 86
15473 AAGAACATCT
* ** * *
15483 CACATGACTTTCTCGTGAAGGGGAGTCATCGAAAGATCATCTCACCTGGTTCAGACCCGTGAAGG
1 CACACGACTTTCTCGTGAAGAAGAGTCATCCAAAGATCATCTCACCTGGTTCAGACCCGCGAAGG
15548 GGAACCACCTGAAGAATATAC
66 GGAACCACCTGAAGAATATAC
15569 CACACGACTTTCTCGTGAAGAAGAGTCATCCAAAGATCATCTCACCTGGTTCAGACCCGCGAAGG
1 CACACGACTTTCTCGTGAAGAAGAGTCATCCAAAGATCATCTCACCTGGTTCAGACCCGCGAAGG
15634 GGAACCACCTGAAGAATATAC
66 GGAACCACCTGAAGAATATAC
15655 CAC
1 CAC
15658 TTGGCTTTCC
Statistics
Matches: 84, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
86 84 1.00
ACGTcount: A:0.31, C:0.27, G:0.22, T:0.19
Consensus pattern (86 bp):
CACACGACTTTCTCGTGAAGAAGAGTCATCCAAAGATCATCTCACCTGGTTCAGACCCGCGAAGG
GGAACCACCTGAAGAATATAC
Found at i:15690 original size:86 final size:86
Alignment explanation
Indices: 15514--15674 Score: 250
Period size: 86 Copynumber: 1.9 Consensus size: 86
15504 GGAGTCATCG
*
15514 AAAGATCATCTCACCTGGTTCAGACCCGTGAAGGGGAACCACCTGAAGAATATACCACACGACTT
1 AAAGATCATCTCACCTGGTTCAGACCCGCGAAGGGGAACCACCTGAAGAATATACCACACGACTT
* * * *
15579 TCTCGTGAAGAAGAGTCATCC
66 TCCCCTGAAGAAGAATCAACC
** *
15600 AAAGATCATCTCACCTGGTTCAGACCCGCGAAGGGGAACCACCTGAAGAATATACCACTTGGCTT
1 AAAGATCATCTCACCTGGTTCAGACCCGCGAAGGGGAACCACCTGAAGAATATACCACACGACTT
15665 TCCCCTGAAG
66 TCCCCTGAAG
15675 GGGAATAGAC
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
86 69 1.00
ACGTcount: A:0.31, C:0.28, G:0.21, T:0.20
Consensus pattern (86 bp):
AAAGATCATCTCACCTGGTTCAGACCCGCGAAGGGGAACCACCTGAAGAATATACCACACGACTT
TCCCCTGAAGAAGAATCAACC
Found at i:16083 original size:199 final size:200
Alignment explanation
Indices: 15743--16722 Score: 1009
Period size: 199 Copynumber: 4.9 Consensus size: 200
15733 TAGAGGAACC
* * * * * * *
15743 GTTTACAACATAGCTCAAGGCGATAAAGGTTATTTGTCAACAAAACTATCTAGTTTGATTCCATT
1 GTTTACAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAACTTTCTAGTTCGATTCCATT
* * ***
15808 CAGCTCGAAGGCATATCAACCGCATGGTAGCAATGAGGAACTATTTTTTAGTTGAAGTTTAAACC
66 CAGCTCGAAGGCATATCAACCGCATGGTAGCAATGAAGAACTACTTTCCGGTTGAAGTTTAAACC
* * * * * *
15873 GATGTCTTTAAGTTAAGAAGAATACCTAGGTTGGTTGCG-TTTAACAACAAGAAACTATATCCCA
131 GAGGTCTTTAAGTCAAGAAGAAGACCTAGGTTGGCTGCGATTTAGCAACAAGAAACTATCTCCCA
**
15937 ACCGA
196 ACAAA
*
15942 GTTTACAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAACTTTCTAGTTCGATTTCATT
1 GTTTACAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAACTTTCTAGTTCGATTCCATT
**
16007 CAGCTCGAAGGCATATCAACCGCATGGTAGCAATGAAGAACTACTTTTTGGTTGAAGTTTAAACC
66 CAGCTCGAAGGCATATCAACCGCATGGTAGCAATGAAGAACTACTTTCCGGTTGAAGTTTAAACC
* * * * *
16072 AAGGTCTTTAAGTC------AAGACCTAGGTTGGTTGTGATTTAGCAACAAGGAACTATCTCACA
131 GAGGTCTTTAAGTCAAGAAGAAGACCTAGGTTGGCTGCGATTTAGCAACAAGAAACTATCTCCCA
*
16131 GCAAA
196 ACAAA
* *
16136 GTTTACAGCATAACTCAAGGCGAGAAGGGCTATCTATCAACAAAACTTT-TGAGTTCGATTCCAT
1 GTTTACAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAACTTTCT-AGTTCGATTCCAT
* *
16200 TCAGCTCGAAGGTC-TATCAACCGCATGGTAGCAATGAGGAACTACTTTCCGATTGAAGTTTAAA
65 TCAGCTCGAAGG-CATATCAACCGCATGGTAGCAATGAAGAACTACTTTCCGGTTGAAGTTTAAA
* * * *
16264 CTGAGGTCTTTAAGTCAAGAAGAAGACCTCGGTTGGCTGCGATTTAGCAACATGGAACTATCTCC
129 CCGAGGTCTTTAAGTCAAGAAGAAGACCTAGGTTGGCTGCGATTTAGCAACAAGAAACTATCTCC
* *
16329 CAGCCGAA
194 CA-ACAAA
* * * *
16337 -TTTACAACATAGCTTAAGGCGAGAAGGGCTATCTGT-AAAAAAACTTTCGAGTTCGATTCCATT
1 GTTTACAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAACTTTCTAGTTCGATTCCATT
* * * * * * * *
16400 CAGATTGAAGGCATATCAACCACTTGGTAGCAACG-AGAAAATACATTCCGGTTCAAGTTTAAAC
66 CAGCTCGAAGGCATATCAACCGCATGGTAGCAATGAAG-AACTACTTTCCGGTTGAAGTTTAAAC
* * * * * *
16464 TGAGGTCTTTACGTCAAAAAGAAGACCTAGGTTAGCTGTGATTTAGCAACAA-AGATCTATCTCC
130 CGAGGTCTTTAAGTCAAGAAGAAGACCTAGGTTGGCTGCGATTTAGCAACAAGA-AACTATCTCC
16528 CAGA-AAA
194 CA-ACAAA
* * * * * * * *
16535 ATTTATAGTATAACTCAAGACGAGAAGGGCTATCTGTCAACAAAAACCTTCAAGTTCGATTCTAT
1 GTTTACAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAAC-AAAACTTTCTAGTTCGATTCCAT
* * ** * * * * *
16600 TCAGCTTGAGGGCATATCAACCATATGGTGGC-TTCGAAGAACTACTTTCCGATTAAATTTTCAA
65 TCAGCTCGAAGGCATATCAACCGCATGGTAGCAAT-GAAGAACTACTTTCCGGTTGAAGTTT-AA
* ** * * * * * ** *
16664 ACCGAGGTATTTAAACCGACAAAAAGACCAAGGTTGACTATGATTTGGCAACAAGAAAC
128 ACCGAGGTCTTTAAGTCAAGAAGAAGACCTAGGTTGGCTGCGATTTAGCAACAAGAAAC
16723 CATATTCCGA
Statistics
Matches: 659, Mismatches: 101, Indels: 39
0.82 0.13 0.05
Matches are distributed among these distances:
193 18 0.03
194 154 0.23
195 1 0.00
198 4 0.01
199 292 0.44
200 74 0.11
201 68 0.10
202 47 0.07
203 1 0.00
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (200 bp):
GTTTACAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAACTTTCTAGTTCGATTCCATT
CAGCTCGAAGGCATATCAACCGCATGGTAGCAATGAAGAACTACTTTCCGGTTGAAGTTTAAACC
GAGGTCTTTAAGTCAAGAAGAAGACCTAGGTTGGCTGCGATTTAGCAACAAGAAACTATCTCCCA
ACAAA
Found at i:16472 original size:393 final size:393
Alignment explanation
Indices: 15743--16677 Score: 1108
Period size: 393 Copynumber: 2.4 Consensus size: 393
15733 TAGAGGAACC
* * * * * * * *
15743 GTTTACAACATAGCTCAAGGCGATAAAGGTTATTTGTCAACAAAACTATCTAGTTTGATTCCATT
1 GTTTACAGCATAACTCAAGGCGAGAAGGGCTATCTGTCAACAAAACT-TTTAGTTCGATTCCATT
***
15808 CAGCTCGAAGGCATATCAACCGCATGGTAGCAATGAGGAACTA-TTTTTTAGTTGAAGTTTAAAC
65 CAGCTCGAAGGCATATCAACCGCATGGTAGCAATGAGGAACTACTTTCCGA-TTGAAGTTTAAAC
* * * *
15872 CGATGTCTTTAAGTTAAGAAGAATACCTAGGTTGGTTGCGTTTAACAACAAGAAACTATATCCCA
129 CGAGGTCTTTAAGTCAAGAAGAAGACCTAGGTTGGCTGCGTTTAACAACAAGAAACTATATCCCA
* * * *
15937 ACCGAGTTTACAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAACTTTCTAGTTCGATT
194 ACCGAATTTACAACATAGCTCAAGGCGAGAAGGGCTATCTGTCAAAAAAACTTTCGAGTTCGATT
* * * * * * ** *
16002 TCATTCAGCTCGAAGGCATATCAACCGCATGGTAGCAATGAAGAACTACTTTTTGGTTGAAGTTT
259 CCATTCAGATCGAAGGCATATCAACCACATGGTAGCAACGAAGAAATACATTCCGGTTCAAGTTT
* * *
16067 AAACCAAGGTCTTTAAGTC-AAGACCTAGGTTGGTTGTGATTTAGCAACAAGGAACTATCTCACA
324 AAACCAAGGTCTTTAAGTCAAAGACCTAGGTTAGCTGTGATTTAGCAACAAAGAACTATCTCACA
*
16131 GCAAA
389 GAAAA
*
16136 GTTTACAGCATAACTCAAGGCGAGAAGGGCTATCTATCAACAAAACTTTTGAGTTCGATTCCATT
1 GTTTACAGCATAACTCAAGGCGAGAAGGGCTATCTGTCAACAAAACTTTT-AGTTCGATTCCATT
16201 CAGCTCGAAGGTC-TATCAACCGCATGGTAGCAATGAGGAACTACTTTCCGATTGAAGTTTAAAC
65 CAGCTCGAAGG-CATATCAACCGCATGGTAGCAATGAGGAACTACTTTCCGATTGAAGTTTAAAC
* * * * * *
16265 TGAGGTCTTTAAGTCAAGAAGAAGACCTCGGTTGGCTGCGATTTAGCAACATGGAACTATCTCCC
129 CGAGGTCTTTAAGTCAAGAAGAAGACCTAGGTTGGCTGCG-TTTAACAACAAGAAACTATATCCC
* *
16330 AGCCGAATTTACAACATAGCTTAAGGCGAGAAGGGCTATCTGT-AAAAAAACTTTCGAGTTCGAT
193 AACCGAATTTACAACATAGCTCAAGGCGAGAAGGGCTATCTGTCAAAAAAACTTTCGAGTTCGAT
* *
16394 TCCATTCAGATTGAAGGCATATCAACCACTTGGTAGCAACG-AGAAAATACATTCCGGTTCAAGT
258 TCCATTCAGATCGAAGGCATATCAACCACATGGTAGCAACGAAG-AAATACATTCCGGTTCAAGT
** * *
16458 TTAAACTGAGGTCTTTACGTCAAAAAGAAGACCTAGGTTAGCTGTGATTTAGCAACAAAGATCTA
322 TTAAACCAAGGTCTTTAAGTC----A-AAGACCTAGGTTAGCTGTGATTTAGCAACAAAGAACTA
*
16523 TCTCCCAGAAAA
382 TCTCACAGAAAA
* * * * ** *
16535 ATTTATAGTATAACTCAAGACGAGAAGGGCTATCTGTCAACAAAAACCTTCAAGTTCGATTCTAT
1 GTTTACAGCATAACTCAAGGCGAGAAGGGCTATCTGTCAAC-AAAA-CTTTTAGTTCGATTCCAT
* * ** * * * * *
16600 TCAGCTTGAGGGCATATCAACCATATGGTGGC-TTCGAAGAACTACTTTCCGATTAAATTTTCAA
64 TCAGCTCGAAGGCATATCAACCGCATGGTAGCAAT-GAGGAACTACTTTCCGATTGAAGTTT-AA
*
16664 ACCGAGGTATTTAA
127 ACCGAGGTCTTTAA
16678 ACCGACAAAA
Statistics
Matches: 459, Mismatches: 67, Indels: 24
0.83 0.12 0.04
Matches are distributed among these distances:
392 4 0.01
393 228 0.50
394 64 0.14
399 82 0.18
400 64 0.14
401 17 0.04
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (393 bp):
GTTTACAGCATAACTCAAGGCGAGAAGGGCTATCTGTCAACAAAACTTTTAGTTCGATTCCATTC
AGCTCGAAGGCATATCAACCGCATGGTAGCAATGAGGAACTACTTTCCGATTGAAGTTTAAACCG
AGGTCTTTAAGTCAAGAAGAAGACCTAGGTTGGCTGCGTTTAACAACAAGAAACTATATCCCAAC
CGAATTTACAACATAGCTCAAGGCGAGAAGGGCTATCTGTCAAAAAAACTTTCGAGTTCGATTCC
ATTCAGATCGAAGGCATATCAACCACATGGTAGCAACGAAGAAATACATTCCGGTTCAAGTTTAA
ACCAAGGTCTTTAAGTCAAAGACCTAGGTTAGCTGTGATTTAGCAACAAAGAACTATCTCACAGA
AAA
Found at i:17720 original size:18 final size:18
Alignment explanation
Indices: 17697--17739 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
17687 CTTTAGATTA
* *
17697 TTTATTTAATTATTTTCT
1 TTTATTTAATTATTATCC
*
17715 TTTATTTAATTCTTATCC
1 TTTATTTAATTATTATCC
17733 TTTATTT
1 TTTATTT
17740 TAAAAACAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.21, C:0.09, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTATTTAATTATTATCC
Found at i:17980 original size:16 final size:16
Alignment explanation
Indices: 17939--17980 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
17929 ATTTTTTTCT
*
17939 TTTAACATTTTTTATA
1 TTTAACATTTTTTAAA
*
17955 TATAACATTTTTTAAA
1 TTTAACATTTTTTAAA
*
17971 TTTAATATTT
1 TTTAACATTT
17981 CCATCTTTGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.60
Consensus pattern (16 bp):
TTTAACATTTTTTAAA
Found at i:23256 original size:86 final size:86
Alignment explanation
Indices: 23161--23348 Score: 295
Period size: 86 Copynumber: 2.2 Consensus size: 86
23151 TCTCACATAT
* * *
23161 TTTCCCGTGAAGGGGAGTCATCGAAAGATCATCTCACCTGGTTCAGACCCGCGAAGGGGAACTAC
1 TTTCCCGTGAAGGGGAGTCATCCAAAGATCATCTCACATGGTTCAGACCCGCGAAGGGGAACCAC
*
23226 CTGAAGAATATACCACACGAC
66 CTAAAGAATATACCACACGAC
* * *
23247 TTTCCCGTGAAGAGGAGTCATCCAAATATTATCTCACATGGTTCAGACCCGCGAAGGGGAACCAC
1 TTTCCCGTGAAGGGGAGTCATCCAAAGATCATCTCACATGGTTCAGACCCGCGAAGGGGAACCAC
**
23312 CTAAAGAATATACCACTTGAC
66 CTAAAGAATATACCACACGAC
23333 TTTCCCGTGAAGGGGA
1 TTTCCCGTGAAGGGGA
23349 ATCAACTAAA
Statistics
Matches: 92, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
86 92 1.00
ACGTcount: A:0.30, C:0.26, G:0.23, T:0.21
Consensus pattern (86 bp):
TTTCCCGTGAAGGGGAGTCATCCAAAGATCATCTCACATGGTTCAGACCCGCGAAGGGGAACCAC
CTAAAGAATATACCACACGAC
Found at i:24071 original size:200 final size:200
Alignment explanation
Indices: 23415--24349 Score: 1136
Period size: 200 Copynumber: 4.7 Consensus size: 200
23405 AGAGGAACCG
* * *
23415 TTTACAGCATAGCACAAGGCGAGAA-AGATTATCTCTCAACAAAACTATT-GAGTTTGATTCCAT
1 TTTACAGCATAGCTCAAGGCGAGAAGAGA-TATCTGTCAAAAAAACT-TTCGAGTTTGATTCCAT
* *
23478 TCAGCTCGAAGGCATATCAACCGCATGGTAGCAACGAGGAACTATTTTCTGGTTGAAGTTTAAAC
64 TCAGCTCGAAGGCATATCAACCGCATGGTAGCAACGAGGAACTACTTTCCGGTTGAAGTTTAAAC
* * * *
23543 CGATGTCTTTAAGTCAAGAATAAGACCTAGGTTGGTTGCG-TTTAGCAACAAAGAACTATCTCCC
129 TGAGGTCTTTAAGTCAAGAAGAAGACCTAGGTTGGTTGCGATTTAGCAACAAGGAACTATCTCCC
*
23607 A-ACCGAG
194 AGA-CGAA
* * * * * * * *
23614 TTTACAGAATAGCTCAAGGCGATAAGGGTTATCTGTTAACAAAACTTTCGAGTTCGATTTCATTC
1 TTTACAGCATAGCTCAAGGCGAGAAGAGATATCTGTCAAAAAAACTTTCGAGTTTGATTCCATTC
*
23679 AGCTCGAAGGCATATCAACCGCATGGTAGCAACGAGGAACTACTTTTCGGTTGAAGTTTAAACTG
66 AGCTCGAAGGCATATCAACCGCATGGTAGCAACGAGGAACTACTTTCCGGTTGAAGTTTAAACTG
*
23744 AGGTCTTTAAGTC------AAGACCTAGGTTGGTTGCGATTTAGCAACAAGGAACTATCTCACAG
131 AGGTCTTTAAGTCAAGAAGAAGACCTAGGTTGGTTGCGATTTAGCAACAAGGAACTATCTCCCAG
* *
23803 CCGAG
196 ACGAA
* * * * *
23808 TTTACAACATAGCTCAAGGCGAGAAGAGCTATCTATCAATAAAACTTTCGA-TTTCAATTCCATT
1 TTTACAGCATAGCTCAAGGCGAGAAGAGATATCTGTCAAAAAAACTTTCGAGTTT-GATTCCATT
* * * * * *
23872 CAGCTCAAAGGCATATGAACCACGTAGTAGCAACGAGGAACTTCTTTCCGGTTGAAGTTTAAACT
65 CAGCTCGAAGGCATATCAACCGCATGGTAGCAACGAGGAACTACTTTCCGGTTGAAGTTTAAACT
* * *
23937 GAGGTCTTTAAGTCAAGAAGAAGACCTGGGTTGGCTGTGATTTAGCAACAAGGAACTATCTCCCA
130 GAGGTCTTTAAGTCAAGAAGAAGACCTAGGTTGGTTGCGATTTAGCAACAAGGAACTATCTCCCA
**
24002 GAAAAA
195 GACGAA
* * * *
24008 ATTACAGCATAGCTCAAGGTGATAAGAGATATATGTCAAAAAAACTTTCGAGTTTGATTCCATTC
1 TTTACAGCATAGCTCAAGGCGAGAAGAGATATCTGTCAAAAAAACTTTCGAGTTTGATTCCATTC
* ** * *
24073 AGATCGAAGGCATATCAACCGTTTGGTAGCAACGAGGAAATACTTTCCGCTTGAAGTTTAAACTG
66 AGCTCGAAGGCATATCAACCGCATGGTAGCAACGAGGAACTACTTTCCGGTTGAAGTTTAAACTG
* ** * *
24138 AGGTCTTTAGGTCAAGAAGAAGACCTAGGTTGGTTGTTATTTAACAATAAGGAACTATCTCCCAG
131 AGGTCTTTAAGTCAAGAAGAAGACCTAGGTTGGTTGCGATTTAGCAACAAGGAACTATCTCCCAG
*
24203 CCGAA
196 ACGAA
* * * * *
24208 TTTACAGAATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTCCATT
1 TTTACAGCATAGCTCAAGGCGAGAAGAGATATCTGTCAA-AAAAACTTTCGAGTTTGATTCCATT
* ** ** * * *
24273 CAGCTCGAGGGCATATCAACCATATGGTAGCATTGACGAACTACTTTCTGGTTGAATTTTCAAAC
65 CAGCTCGAAGGCATATCAACCGCATGGTAGCAACGAGGAACTACTTTCCGGTTGAAGTTT-AAAC
*
24338 CGAGGTCTTTAA
129 TGAGGTCTTTAA
24350 ACCGAGAAAA
Statistics
Matches: 629, Mismatches: 93, Indels: 25
0.84 0.12 0.03
Matches are distributed among these distances:
193 21 0.03
194 149 0.24
198 2 0.00
199 124 0.20
200 244 0.39
201 75 0.12
202 14 0.02
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (200 bp):
TTTACAGCATAGCTCAAGGCGAGAAGAGATATCTGTCAAAAAAACTTTCGAGTTTGATTCCATTC
AGCTCGAAGGCATATCAACCGCATGGTAGCAACGAGGAACTACTTTCCGGTTGAAGTTTAAACTG
AGGTCTTTAAGTCAAGAAGAAGACCTAGGTTGGTTGCGATTTAGCAACAAGGAACTATCTCCCAG
ACGAA
Found at i:24141 original size:394 final size:394
Alignment explanation
Indices: 23414--24349 Score: 1184
Period size: 394 Copynumber: 2.4 Consensus size: 394
23404 TAGAGGAACC
* * * * *
23414 GTTTACAGCATAGCACAAGGCGAGAA-AGATTATCTCTCAACAAAACTATT-GAGTTT-GATTCC
1 GTTTACAACATAGCTCAAGGCGAGAAGAG-CTATCTATCAAAAAAACT-TTCGA-TTTCGATTCC
*
23476 ATTCAGCTCGAAGGCATATCAACCGCATGGTAGCAACGAGGAACTAT-TTTCTGGTTGAAGTTTA
63 ATTCAGCTCGAAGGCATATCAACCACATGGTAGCAACGAGGAACT-TCTTTCTGGTTGAAGTTTA
* * *
23540 AACCGATGTCTTTAAGTCAAGAATAAGACCTAGGTTGGTTGCGTTTAGCAACAAAGAACTATCTC
127 AACCGAGGTCTTTAAGTCAAGAAGAAGACCTAGGTTGGCTGCGTTTAGCAACAAAGAACTATCTC
** ** * * * * *
23605 CCAACCGAGTTTACAGAATAGCTCAAGGCGATAAGGGTTATCTGTTAACAAAACTTTCGAGTTCG
192 CCAACAAAAATTACAGAATAGCTCAAGGCGATAAGAGATATATGTCAAAAAAACTTTCGAGTTCG
* * * * *
23670 ATTTCATTCAGCTCGAAGGCATATCAACCGCATGGTAGCAACGAGGAACTACTTTTCGGTTGAAG
257 ATTCCATTCAGATCGAAGGCATATCAACCGCATGGTAGCAACGAGGAAATACTTTCCGCTTGAAG
*
23735 TTTAAACTGAGGTCTTTAAGTC-AAGACCTAGGTTGGTTGCGATTTAGCAACAAGGAACTATCTC
322 TTTAAACTGAGGTCTTTAAGTCAAAGACCTAGGTTGGTTGCGATTTAACAACAAGGAACTATCTC
23799 ACAGCCGA
387 ACAGCCGA
* *
23807 GTTTACAACATAGCTCAAGGCGAGAAGAGCTATCTATCAATAAAACTTTCGATTTCAATTCCATT
1 GTTTACAACATAGCTCAAGGCGAGAAGAGCTATCTATCAAAAAAACTTTCGATTTCGATTCCATT
* * * * * *
23872 CAGCTCAAAGGCATATGAACCACGTAGTAGCAACGAGGAACTTCTTTCCGGTTGAAGTTTAAACT
66 CAGCTCGAAGGCATATCAACCACATGGTAGCAACGAGGAACTTCTTTCTGGTTGAAGTTTAAACC
* * *
23937 GAGGTCTTTAAGTCAAGAAGAAGACCTGGGTTGGCTGTGATTTAGCAACAAGGAACTATCTCCCA
131 GAGGTCTTTAAGTCAAGAAGAAGACCTAGGTTGGCTGCG-TTTAGCAACAAAGAACTATCTCCCA
* * *
24002 GA-AAAAATTACAGCATAGCTCAAGGTGATAAGAGATATATGTCAAAAAAACTTTCGAGTTTGAT
195 -ACAAAAATTACAGAATAGCTCAAGGCGATAAGAGATATATGTCAAAAAAACTTTCGAGTTCGAT
**
24066 TCCATTCAGATCGAAGGCATATCAACCGTTTGGTAGCAACGAGGAAATACTTTCCGCTTGAAGTT
259 TCCATTCAGATCGAAGGCATATCAACCGCATGGTAGCAACGAGGAAATACTTTCCGCTTGAAGTT
* ** *
24131 TAAACTGAGGTCTTTAGGTCAAGAAGAAGACCTAGGTTGGTTGTTATTTAACAATAAGGAACTAT
324 TAAACTGAGGTCTTTAAGTC----A-AAGACCTAGGTTGGTTGCGATTTAACAACAAGGAACTAT
*
24196 CTCCCAGCCGA
384 CTCACAGCCGA
* * * * *
24207 ATTTACAGA-ATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTCCA
1 GTTTACA-ACATAGCTCAAGGCGAGAAGAGCTATCTATCAA-AAAAACTTTCGATTTCGATTCCA
* * ** * * *
24271 TTCAGCTCGAGGGCATATCAACCATATGGTAGCATTGACGAACTACTTTCTGGTTGAATTTTCAA
64 TTCAGCTCGAAGGCATATCAACCACATGGTAGCAACGAGGAACTTCTTTCTGGTTGAAGTTT-AA
24336 ACCGAGGTCTTTAA
128 ACCGAGGTCTTTAA
24350 ACCGAGAAAA
Statistics
Matches: 464, Mismatches: 64, Indels: 21
0.85 0.12 0.04
Matches are distributed among these distances:
392 6 0.01
393 139 0.30
394 153 0.33
395 1 0.00
400 80 0.17
401 70 0.15
402 15 0.03
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (394 bp):
GTTTACAACATAGCTCAAGGCGAGAAGAGCTATCTATCAAAAAAACTTTCGATTTCGATTCCATT
CAGCTCGAAGGCATATCAACCACATGGTAGCAACGAGGAACTTCTTTCTGGTTGAAGTTTAAACC
GAGGTCTTTAAGTCAAGAAGAAGACCTAGGTTGGCTGCGTTTAGCAACAAAGAACTATCTCCCAA
CAAAAATTACAGAATAGCTCAAGGCGATAAGAGATATATGTCAAAAAAACTTTCGAGTTCGATTC
CATTCAGATCGAAGGCATATCAACCGCATGGTAGCAACGAGGAAATACTTTCCGCTTGAAGTTTA
AACTGAGGTCTTTAAGTCAAAGACCTAGGTTGGTTGCGATTTAACAACAAGGAACTATCTCACAG
CCGA
Found at i:24563 original size:19 final size:19
Alignment explanation
Indices: 24539--24576 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
24529 CACAAAAAAT
24539 CGTTACATGAAAAAGGACA
1 CGTTACATGAAAAAGGACA
24558 CGTTACATGAAAAAGGACA
1 CGTTACATGAAAAAGGACA
24577 AAGAGAGACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.16, G:0.21, T:0.16
Consensus pattern (19 bp):
CGTTACATGAAAAAGGACA
Found at i:24718 original size:12 final size:13
Alignment explanation
Indices: 24691--24719 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
24681 TCAATTAAGA
24691 TTTAATATATTAT
1 TTTAATATATTAT
24704 TTTAA-ATATTAT
1 TTTAATATATTAT
24716 TTTA
1 TTTA
24720 TTTTATCTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TTTAATATATTAT
Found at i:25415 original size:18 final size:18
Alignment explanation
Indices: 25392--25434 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
25382 CTTTAGATTA
*
25392 TTTATTTAATTATTTTCT
1 TTTATTTAATTATTATCT
*
25410 TTTATTTAATTCTTATCT
1 TTTATTTAATTATTATCT
25428 TTTATTT
1 TTTATTT
25435 TAAAAATAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTATTTAATTATTATCT
Found at i:25512 original size:5 final size:5
Alignment explanation
Indices: 25483--25571 Score: 56
Period size: 5 Copynumber: 16.6 Consensus size: 5
25473 CTATTATTTA
* *
25483 TTATT TTATT ATATT TTCATTTT TTATT TTATT TTGTT TTATCT TTATT
1 TTATT TTATT TTATT TT-A--TT TTATT TTATT TTATT TTAT-T TTATT
* *
25532 TTCACACTT TT-TT TTATT TTGTT TTATT TT-TT TTCTT TTA
1 TT---A-TT TTATT TTATT TTATT TTATT TTATT TTATT TTA
25572 ACACTTTTTA
Statistics
Matches: 67, Mismatches: 7, Indels: 20
0.71 0.07 0.21
Matches are distributed among these distances:
4 8 0.12
5 43 0.64
6 6 0.09
7 1 0.01
8 5 0.07
9 4 0.06
ACGTcount: A:0.16, C:0.07, G:0.02, T:0.75
Consensus pattern (5 bp):
TTATT
Found at i:25522 original size:16 final size:16
Alignment explanation
Indices: 25504--25533 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
25494 TATTTTCATT
25504 TTTTAT-TTTATTTTG
1 TTTTATCTTTATTTTG
25519 TTTTATCTTTATTTT
1 TTTTATCTTTATTTT
25534 CACACTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.13, C:0.03, G:0.03, T:0.80
Consensus pattern (16 bp):
TTTTATCTTTATTTTG
Found at i:25533 original size:34 final size:32
Alignment explanation
Indices: 25486--25570 Score: 102
Period size: 34 Copynumber: 2.6 Consensus size: 32
25476 TTATTTATTA
*
25486 TTTTATTATATTTTCATTTTTTATTTTATTTTG
1 TTTTATTTTATTTTCATTTTTT-TTTTATTTTG
**
25519 TTTTATCTTTATTTTCACACTTTTTTTTATTTTG
1 TTTTAT-TTTATTTTCA-TTTTTTTTTTATTTTG
25553 TTTTATTTT-TTTTC-TTTT
1 TTTTATTTTATTTTCATTTT
25571 AACACTTTTT
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
30 2 0.04
32 5 0.11
33 9 0.20
34 25 0.56
35 4 0.09
ACGTcount: A:0.14, C:0.07, G:0.02, T:0.76
Consensus pattern (32 bp):
TTTTATTTTATTTTCATTTTTTTTTTATTTTG
Found at i:25565 original size:14 final size:15
Alignment explanation
Indices: 25504--25571 Score: 59
Period size: 14 Copynumber: 4.3 Consensus size: 15
25494 TATTTTCATT
*
25504 TTTTATTTTATTTTG
1 TTTTATTTTATTTTC
25519 TTTTATCTTTATTTTCACAC
1 TTTTAT-TTTATTTT----C
*
25539 TTTT-TTTTATTTTG
1 TTTTATTTTATTTTC
25553 TTTTATTTT-TTTTC
1 TTTTATTTTATTTTC
25567 TTTTA
1 TTTTA
25572 ACACTTTTTA
Statistics
Matches: 44, Mismatches: 3, Indels: 13
0.73 0.05 0.22
Matches are distributed among these distances:
14 13 0.30
15 10 0.23
16 8 0.18
18 8 0.18
19 1 0.02
20 4 0.09
ACGTcount: A:0.13, C:0.07, G:0.03, T:0.76
Consensus pattern (15 bp):
TTTTATTTTATTTTC
Found at i:37339 original size:7 final size:7
Alignment explanation
Indices: 37329--37359 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
37319 TTAAAATTTA
37329 AAATATG
1 AAATATG
37336 AAATATG
1 AAATATG
37343 AAATATG
1 AAATATG
37350 AAATATG
1 AAATATG
37357 AAA
1 AAA
37360 AAAATTAAAT
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:0.61, C:0.00, G:0.13, T:0.26
Consensus pattern (7 bp):
AAATATG
Found at i:39319 original size:31 final size:30
Alignment explanation
Indices: 39284--39369 Score: 84
Period size: 31 Copynumber: 2.8 Consensus size: 30
39274 ATTGTAAGAT
39284 GTCTGAACAATATGTTTCCTAAATTCTATG-C
1 GTCTGAACAATATGTTTCCTAAA--CTATGAC
* * * * *
39315 GTCTGAGCAATATATTTCATGAACTATGATT
1 GTCTGAACAATATGTTTCCTAAACTATGA-C
*
39346 GTATGAACAATATGTTTCCTAAAC
1 GTCTGAACAATATGTTTCCTAAAC
39370 CGTGACATTC
Statistics
Matches: 43, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
29 5 0.12
31 38 0.88
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (30 bp):
GTCTGAACAATATGTTTCCTAAACTATGAC
Found at i:39406 original size:31 final size:31
Alignment explanation
Indices: 39378--39470 Score: 123
Period size: 32 Copynumber: 3.0 Consensus size: 31
39368 ACCGTGACAT
39378 TCTAAACGATATGTTTTTTGAATTGTGACTA
1 TCTAAACGATATGTTTTTTGAATTGTGACTA
* * * * *
39409 ACTGAACAATATGTTTTTTTGAGTTGTTACTA
1 TCTAAACGATATG-TTTTTTGAATTGTGACTA
*
39441 TCTAAACGATATGTTTTTTGAACTGTGACT
1 TCTAAACGATATGTTTTTTGAATTGTGACT
39471 GTTTGTATAT
Statistics
Matches: 50, Mismatches: 11, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
31 24 0.48
32 26 0.52
ACGTcount: A:0.28, C:0.11, G:0.16, T:0.45
Consensus pattern (31 bp):
TCTAAACGATATGTTTTTTGAATTGTGACTA
Found at i:42157 original size:43 final size:43
Alignment explanation
Indices: 42089--42184 Score: 111
Period size: 43 Copynumber: 2.2 Consensus size: 43
42079 GGGTAGACTT
* * * *
42089 GGGTCACATAACATCAACATTTCCCAAGTATCTCAGGCGAGGTTC
1 GGGTCAC--AACATCAACATCTCCCAAATACCTCAGGCGAGGTAC
* * *
42134 GGGTCACAACATCGACATCTCCCAAATACCTTAGGCTAGGTAC
1 GGGTCACAACATCAACATCTCCCAAATACCTCAGGCGAGGTAC
42177 GGGTCACA
1 GGGTCACA
42185 CAATATCAGC
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
43 37 0.84
45 7 0.16
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (43 bp):
GGGTCACAACATCAACATCTCCCAAATACCTCAGGCGAGGTAC
Found at i:50021 original size:112 final size:112
Alignment explanation
Indices: 49824--50389 Score: 1010
Period size: 112 Copynumber: 5.1 Consensus size: 112
49814 CCTCGCCGAT
* * * *
49824 TCTATATTTGTTGCTAATATTGTCTCCATTTTAATCATACTTTTAATTATTGATTTATTATATTT
1 TCTATATCTGTTGCTAATCTTGGCTCCATTTTAGTCATACTTTTAATTATTGATTTATTATATTT
* *
49889 ATGTCTTTAAAGATT-AACATTAATTTTTATTCAACTTCTTATTCATG
66 ATGTCTTTAAAG-TTGAACATTAATTTTTATTTAACTTTTTATTCATG
** *
49936 TCTATATCTGTTGCTAATCTAAGCTCCATTTTAGTCATATTTTTAATTATTGATTTATTATATTT
1 TCTATATCTGTTGCTAATCTTGGCTCCATTTTAGTCATACTTTTAATTATTGATTTATTATATTT
*
50001 ATGTCTTTAAAGTTGAACATTAATTTTTATTTGACTTTTTATTCATG
66 ATGTCTTTAAAGTTGAACATTAATTTTTATTTAACTTTTTATTCATG
*
50048 TCTCTATCTGTTGCTAATCTTGGCTCCATTTTAGTCATACTTTTAATTATTGATTTATTATATTT
1 TCTATATCTGTTGCTAATCTTGGCTCCATTTTAGTCATACTTTTAATTATTGATTTATTATATTT
50113 ATGTCTTTAAAGTTGAACATTAATTTTTATTTAACTTTTTATTCATG
66 ATGTCTTTAAAGTTGAACATTAATTTTTATTTAACTTTTTATTCATG
50160 TCTATATCTGTTGCTAATCTTGGCTCCATTTTAGTCATACTTTTAATTATTGATTTATTATATTT
1 TCTATATCTGTTGCTAATCTTGGCTCCATTTTAGTCATACTTTTAATTATTGATTTATTATATTT
50225 ATGTCTTTAAAGTTGAACATTAATTTTTATTTAACTTTTTATTCATG
66 ATGTCTTTAAAGTTGAACATTAATTTTTATTTAACTTTTTATTCATG
50272 TCTATATCTGTTGCTAATCTTGGCTCCATTTTAGTCATACTTTTAATTATTGATTTATTATATTT
1 TCTATATCTGTTGCTAATCTTGGCTCCATTTTAGTCATACTTTTAATTATTGATTTATTATATTT
50337 ATGTCTTTAAAGTTGAACATTAATTTTTATTTAACTTTTTATTCATG
66 ATGTCTTTAAAGTTGAACATTAATTTTTATTTAACTTTTTATTCATG
50384 T-TATAT
1 TCTATAT
50390 GATATTTATT
Statistics
Matches: 437, Mismatches: 16, Indels: 3
0.96 0.04 0.01
Matches are distributed among these distances:
111 7 0.02
112 430 0.98
ACGTcount: A:0.27, C:0.11, G:0.08, T:0.54
Consensus pattern (112 bp):
TCTATATCTGTTGCTAATCTTGGCTCCATTTTAGTCATACTTTTAATTATTGATTTATTATATTT
ATGTCTTTAAAGTTGAACATTAATTTTTATTTAACTTTTTATTCATG
Found at i:50550 original size:20 final size:20
Alignment explanation
Indices: 50527--50650 Score: 160
Period size: 20 Copynumber: 6.2 Consensus size: 20
50517 GTTTTCAAAT
*
50527 TCGCAACTCG-ATTATGTAAA
1 TCGCAACGCGAATT-TGTAAA
** * **
50547 TCGCATTGCGATTTTCCAAA
1 TCGCAACGCGAATTTGTAAA
*
50567 TTCGCAACGCGAATATGTAAA
1 -TCGCAACGCGAATTTGTAAA
50588 TCGCAACGCGAATTTGTAAA
1 TCGCAACGCGAATTTGTAAA
50608 TCGCAACGCGAATTTGTAAA
1 TCGCAACGCGAATTTGTAAA
50628 TCGCAACGCGAATTTGTAAA
1 TCGCAACGCGAATTTGTAAA
50648 TCG
1 TCG
50651 TAACACAGAA
Statistics
Matches: 89, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
20 73 0.82
21 16 0.18
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (20 bp):
TCGCAACGCGAATTTGTAAA
Found at i:50573 original size:41 final size:40
Alignment explanation
Indices: 50507--50638 Score: 153
Period size: 40 Copynumber: 3.3 Consensus size: 40
50497 AATTCCTATT
* * *
50507 TCGCAACCCGGTTTTCAAATTCGCAACTCGATTATGTAAA
1 TCGCAACGCGATTTTCAAATTCGCAACGCGATTATGTAAA
** *
50547 TCGCATTGCGATTTTCCAAATTCGCAACGCGAATATGTAAA
1 TCGCAACGCGATTTT-CAAATTCGCAACGCGATTATGTAAA
50588 TCGCAACGCGAATTTGT-AAA-TCGCAACGCGAATT-TGTAAA
1 TCGCAACGCG-ATTT-TCAAATTCGCAACGCG-ATTATGTAAA
50628 TCGCAACGCGA
1 TCGCAACGCGA
50639 ATTTGTAAAT
Statistics
Matches: 79, Mismatches: 9, Indels: 9
0.81 0.09 0.09
Matches are distributed among these distances:
39 1 0.01
40 37 0.47
41 36 0.46
42 4 0.05
43 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (40 bp):
TCGCAACGCGATTTTCAAATTCGCAACGCGATTATGTAAA
Found at i:50672 original size:40 final size:38
Alignment explanation
Indices: 50540--50674 Score: 119
Period size: 40 Copynumber: 3.4 Consensus size: 38
50530 CAACTCGATT
** * ** *
50540 ATGTAAATCGCATTGCGATTTTCCAAATTCGCAACGCGAA
1 ATGTAAATCGCAACGCGAATTTGTAAA-TCGCAACACG-A
*
50580 TATGTAAATCGCAACGCGAATTTGTAAATCGCAACGCGA
1 -ATGTAAATCGCAACGCGAATTTGTAAATCGCAACACGA
*
50619 ATTTGTAAATCGCAACGCGAATTTGTAAATCGTAACACAGA
1 A--TGTAAATCGCAACGCGAATTTGTAAATCGCAACAC-GA
50660 A-GTCAAATTCGCAAC
1 ATGT-AAA-TCGCAAC
50675 ACAAAAGTCA
Statistics
Matches: 82, Mismatches: 7, Indels: 11
0.82 0.07 0.11
Matches are distributed among these distances:
38 3 0.04
39 4 0.05
40 50 0.61
41 25 0.30
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.25
Consensus pattern (38 bp):
ATGTAAATCGCAACGCGAATTTGTAAATCGCAACACGA
Found at i:50759 original size:19 final size:19
Alignment explanation
Indices: 50722--50870 Score: 183
Period size: 19 Copynumber: 7.7 Consensus size: 19
50712 AACACAGAAG
50722 TCAAATTCGCAACACTGAATT
1 TCAAATTCGC-A-ACTGAATT
50743 TCAAATTCGCAACTGAATT
1 TCAAATTCGCAACTGAATT
50762 TCAAATTCGCAACTGAATT
1 TCAAATTCGCAACTGAATT
*
50781 TCAAATTCGTAACTGAATT
1 TCAAATTCGCAACTGAATT
*
50800 TCAAATTAGCAACTGAATT
1 TCAAATTCGCAACTGAATT
* *
50819 TCAAATTCGTAACTCGATTT
1 TCAAATTCGCAACT-GAATT
** *
50839 TTGAATTCGCAACACGAATT
1 TCAAATTCGCAAC-TGAATT
*
50859 T-AATTTCGCAAC
1 TCAAATTCGCAAC
50871 AGGTTTTAGT
Statistics
Matches: 113, Mismatches: 13, Indels: 6
0.86 0.10 0.05
Matches are distributed among these distances:
19 83 0.73
20 20 0.18
21 10 0.09
ACGTcount: A:0.36, C:0.20, G:0.11, T:0.33
Consensus pattern (19 bp):
TCAAATTCGCAACTGAATT
Found at i:50871 original size:19 final size:20
Alignment explanation
Indices: 50563--50871 Score: 203
Period size: 20 Copynumber: 15.7 Consensus size: 20
50553 TGCGATTTTC
*
50563 CAAATTCGCAACGCGAATATGT
1 CAAATTCGCAACACGAAT-T-T
*
50585 -AAA-TCGCAACGCGAATTT
1 CAAATTCGCAACACGAATTT
* *
50603 GTAAA-TCGCAACGCGAATTT
1 -CAAATTCGCAACACGAATTT
* *
50623 GTAAA-TCGCAACGCGAATTT
1 -CAAATTCGCAACACGAATTT
* * *
50643 GTAAA-TCGTAACACAGAA-GT
1 -CAAATTCGCAACAC-GAATTT
* **
50663 CAAATTCGCAACACAAAAGT
1 CAAATTCGCAACACGAATTT
* *
50683 CAAATTCGCAACACAAAAGTT
1 CAAATTCGCAACAC-GAATTT
*
50704 -AAATTCGCAACACAGAA-GT
1 CAAATTCGCAACAC-GAATTT
50723 CAAATTCGCAACACTGAATTT
1 CAAATTCGCAACAC-GAATTT
*
50744 CAAATTCGCAAC-TGAATTT
1 CAAATTCGCAACACGAATTT
*
50763 CAAATTCGCAAC-TGAATTT
1 CAAATTCGCAACACGAATTT
* *
50782 CAAATTCGTAAC-TGAATTT
1 CAAATTCGCAACACGAATTT
* *
50801 CAAATTAGCAAC-TGAATTT
1 CAAATTCGCAACACGAATTT
* * *
50820 CAAATTCGTAACTCGATTTT
1 CAAATTCGCAACACGAATTT
**
50840 TGAATTCGCAACACGAATTT
1 CAAATTCGCAACACGAATTT
*
50860 -AATTTCGCAACA
1 CAAATTCGCAACA
50872 GGTTTTAGTT
Statistics
Matches: 251, Mismatches: 27, Indels: 21
0.84 0.09 0.07
Matches are distributed among these distances:
18 1 0.00
19 87 0.35
20 140 0.56
21 23 0.09
ACGTcount: A:0.39, C:0.21, G:0.14, T:0.26
Consensus pattern (20 bp):
CAAATTCGCAACACGAATTT
Found at i:53968 original size:18 final size:18
Alignment explanation
Indices: 53945--53980 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
53935 AAGCAAAAAG
53945 AAATCAAAATCACAATCA
1 AAATCAAAATCACAATCA
*
53963 AAATCAAAATCTCAATCA
1 AAATCAAAATCACAATCA
53981 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.58, C:0.22, G:0.00, T:0.19
Consensus pattern (18 bp):
AAATCAAAATCACAATCA
Found at i:54273 original size:13 final size:13
Alignment explanation
Indices: 54255--54279 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54245 ATTCGCAACG
54255 CGAAAATCAAAAT
1 CGAAAATCAAAAT
54268 CGAAAATCAAAA
1 CGAAAATCAAAA
54280 ATCACAACGC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.16, G:0.08, T:0.12
Consensus pattern (13 bp):
CGAAAATCAAAAT
Found at i:54313 original size:20 final size:20
Alignment explanation
Indices: 54288--54344 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 20
54278 AAATCACAAC
54288 GCGAATTTGACTTTCGCGTT
1 GCGAATTTGACTTTCGCGTT
* **
54308 GCGAATTTAACTTTAACGTT
1 GCGAATTTGACTTTCGCGTT
*
54328 GCGAATTTGACTATCGC
1 GCGAATTTGACTTTCGC
54345 AACGCGAAAA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.37
Consensus pattern (20 bp):
GCGAATTTGACTTTCGCGTT
Found at i:54351 original size:20 final size:20
Alignment explanation
Indices: 54328--54382 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
54318 CTTTAACGTT
54328 GCGAATTTGACTATCGCAAC
1 GCGAATTTGACTATCGCAAC
*
54348 GCGAA----A--ATCGCAAT
1 GCGAATTTGACTATCGCAAC
54362 GCGAATTTGACTATCGCAAC
1 GCGAATTTGACTATCGCAAC
54382 G
1 G
54383 AGAAAATCGC
Statistics
Matches: 27, Mismatches: 2, Indels: 12
0.66 0.05 0.29
Matches are distributed among these distances:
14 12 0.44
16 1 0.04
18 1 0.04
20 13 0.48
ACGTcount: A:0.33, C:0.24, G:0.22, T:0.22
Consensus pattern (20 bp):
GCGAATTTGACTATCGCAAC
Found at i:54370 original size:34 final size:34
Alignment explanation
Indices: 54327--54394 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
54317 ACTTTAACGT
*
54327 TGCGAATTTGACTATCGCAACGCGAAAATCGCAA
1 TGCGAATTTGACTATCGCAACGAGAAAATCGCAA
54361 TGCGAATTTGACTATCGCAACGAGAAAATCGCAA
1 TGCGAATTTGACTATCGCAACGAGAAAATCGCAA
54395 CACAGATTTG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.37, C:0.22, G:0.21, T:0.21
Consensus pattern (34 bp):
TGCGAATTTGACTATCGCAACGAGAAAATCGCAA
Found at i:54404 original size:34 final size:34
Alignment explanation
Indices: 54329--54412 Score: 116
Period size: 34 Copynumber: 2.5 Consensus size: 34
54319 TTTAACGTTG
* **
54329 CGAATTTGACTATCGCAACGCGAAAATCGCAATG
1 CGAATTTGACTATCGCAACGAGAAAATCGCAACA
54363 CGAATTTGACTATCGCAACGAGAAAATCGCAACA
1 CGAATTTGACTATCGCAACGAGAAAATCGCAACA
*
54397 C-AGATTTGACTTTCGC
1 CGA-ATTTGACTATCGC
54413 GTTGCGAATT
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
33 1 0.02
34 44 0.98
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.23
Consensus pattern (34 bp):
CGAATTTGACTATCGCAACGAGAAAATCGCAACA
Found at i:54423 original size:20 final size:20
Alignment explanation
Indices: 54400--54440 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
54390 CGCAACACAG
54400 ATTTGACTTTCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
54420 ATTTGACTTTCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
54440 A
1 A
54441 AGTGTACATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.17, C:0.20, G:0.24, T:0.39
Consensus pattern (20 bp):
ATTTGACTTTCGCGTTGCGA
Found at i:55743 original size:20 final size:20
Alignment explanation
Indices: 55718--55756 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
55708 TTTTCAAGGG
55718 CATGCACCGATGCACCAATC
1 CATGCACCGATGCACCAATC
* *
55738 CATGCATCGATGCATCAAT
1 CATGCACCGATGCACCAAT
55757 TAATTTCTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.31, C:0.33, G:0.15, T:0.21
Consensus pattern (20 bp):
CATGCACCGATGCACCAATC
Done.